scholarly journals Competition for Light between Toxic and Nontoxic Strains of the Harmful Cyanobacterium Microcystis

2007 ◽  
Vol 73 (9) ◽  
pp. 2939-2946 ◽  
Author(s):  
W. Edwin A. Kardinaal ◽  
Linda Tonk ◽  
Ingmar Janse ◽  
Suzanne Hol ◽  
Pieter Slot ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Internal Transcribed Spacer Region ◽  
Gradient Gel Electrophoresis ◽  
Competition For Light ◽  
Low Levels ◽  
Allelopathic Interactions ◽  
Light Absorbance ◽  
Absorbance Spectra

ABSTRACT The cyanobacterium Microcystis can produce microcystins, a family of toxins that are of major concern in water management. In several lakes, the average microcystin content per cell gradually declines from high levels at the onset of Microcystis blooms to low levels at the height of the bloom. Such seasonal dynamics might result from a succession of toxic to nontoxic strains. To investigate this hypothesis, we ran competition experiments with two toxic and two nontoxic Microcystis strains using light-limited chemostats. The population dynamics of these closely related strains were monitored by means of characteristic changes in light absorbance spectra and by PCR amplification of the rRNA internal transcribed spacer region in combination with denaturing gradient gel electrophoresis, which allowed identification and semiquantification of the competing strains. In all experiments, the toxic strains lost competition for light from nontoxic strains. As a consequence, the total microcystin concentrations in the competition experiments gradually declined. We did not find evidence for allelopathic interactions, as nontoxic strains became dominant even when toxic strains were given a major initial advantage. These findings show that, in our experiments, nontoxic strains of Microcystis were better competitors for light than toxic strains. The generality of this finding deserves further investigation with other Microcystis strains. The competitive replacement of toxic by nontoxic strains offers a plausible explanation for the gradual decrease in average toxicity per cell during the development of dense Microcystis blooms.

A PRELIMINARY CHARACTERISATION OFSYMBIODINIUMDIVERSITY IN SOME COMMON CORALS FROM SINGAPORE

COSMOS ◽  
2016 ◽  
Vol 12 (01) ◽  
pp. 15-27 ◽  
Author(s):  
JANI THUAIBAH ISA TANZIL ◽  
ABIGAYLE PEK KAYE NG ◽  
YI QING TEY ◽  
BEVERLY HSIN YI TAN ◽  
ERIC YAO YUN ◽  
...  
Keyword(s):  
Gel Electrophoresis ◽  
Internal Transcribed Spacer ◽  
Coral Species ◽  
Elevated Temperatures ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Symbiotic Relationship ◽  
Internal Transcribed Spacer Region ◽  
Porites Lutea ◽  
Gradient Gel Electrophoresis ◽  
Response To Stress

The symbiosis between corals and Symbiodinium dinoflagellates is considered a major driver of the distribution and health of reefs worldwide. This study investigated the genetic identities and diversity of Symbiodinium in seven coral species (Porites lutea, Porites lobata, Acropora millepora, Merulina ampliata, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta) from three shallow reefs around Singapore (Kusu Island, Pulau Tekukor, Pulau Satumu). Analyses of 31 colonies using denaturing gradient gel electrophoresis of the nuclear internal transcribed spacer region indicated the dominance of C and D Symbiodinium clades. The latter clade was the predominant symbiont in Pachyseris speciosa collected from Pulau Tekukor but those sampled from Pulau Satumu hosted C27, providing evidence for variable symbiosis in this species. The prevalence of the D clade – noted for their stress tolerance (e.g. to elevated temperatures and sedimentation) – in three of seven coral species examined could underlie the importance of this particular symbiotic relationship for the persistence of Singapore’s impacted reefs. Further characterisation of Symbiodinium communities may provide insights into corals’ response to stress and their bleaching patterns in the future.

scholarly journals Application of Sequence-Dependent Electrophoresis Fingerprinting in Exploring Biodiversity and Population Dynamics of Human Intestinal Microbiota: What Can Be Revealed?

2008 ◽  
Vol 2008 ◽  
pp. 1-26 ◽  
Author(s):  
Geert Huys ◽  
Tom Vanhoutte ◽  
Peter Vandamme
Keyword(s):  
Population Dynamics ◽  
Intestinal Microbiota ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Therapeutic Interventions ◽  
Rrna Gene ◽  
Sequence Dependent ◽  
Human Intestinal Microbiota ◽  
Gradient Gel Electrophoresis ◽  
Community Fingerprinting

Sequence-dependent electrophoresis (SDE) fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE) have become commonplace in the field of molecular microbial ecology. The success of the SDE technology lays in the fact that it allows visualization of the predominant members of complex microbial ecosystems independent of their culturability and without prior knowledge on the complexity and diversity of the ecosystem. Mainly using the prokaryotic 16S rRNA gene as PCR amplification target, SDE-based community fingerprinting turned into one of the leading molecular tools to unravel the diversity and population dynamics of human intestinal microbiota. The first part of this review covers the methodological concept of SDE fingerprinting and the technical hurdles for analyzing intestinal samples. Subsequently, the current state-of-the-art of DGGE and related techniques to analyze human intestinal microbiota from healthy individuals and from patients with intestinal disorders is surveyed. In addition, the applicability of SDE analysis to monitor intestinal population changes upon nutritional or therapeutic interventions is critically evaluated.

Changes in the structure and diversity of bacterial communities during the process of adaptation to organic wastewater

2010 ◽  
Vol 56 (4) ◽  
pp. 352-355 ◽  
Author(s):  
Junmin Li ◽  
Zexin Jin ◽  
Binbin Yu
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Similarity Index ◽  
Pcr Amplification ◽  
Genotypic Diversity ◽  
Diversity Indices ◽  
Inhibitory Effect ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gradient Gel Electrophoresis

To explore changes in the structure and diversity of activated sludge-derived microbial communities during adaptation to gradual increases in the concentration of wastewater, RAPD–PCR and the combination of PCR amplification of 16S rRNA genes with denaturing gradient gel electrophoresis (DGGE) analysis were used. In bacterial communities exposed to 0%, 5%, 10%, 20%, or 40% wastewater, there were 27, 25, 18, 17 and 16 bands, respectively, based on DGGE data, while there were 69, 83, 97, 86, and 88 bands, respectively, based on RAPD data. The community similarity index among bacterial communities during the process of adaptation to different concentrations of wastewater was different based on DGGE and RAPD data. Based on DGGE and RAPD profiles, the Shannon–Weiner and Simpson’s diversity indices decreased sharply upon exposure to 10% wastewater, indicating that 10% wastewater might be a critical point at which the growth of bacteria could be significantly inhibited and the genotypic diversity could change. This indicated that changes in structure and diversity might have an inhibitory effect on the toxicity of organic matter and that selection and adaptation could play important roles in the changes.

Analysis of Fungal Diversity in the Composting by Sequencing of Cloned PCR-Amplified 18S rDNA and Denaturing Gradient Gel Electrophoresis

2011 ◽  
Vol 356-360 ◽  
pp. 1747-1751
Author(s):  
Wan Li ◽  
Xiu Hong Xu ◽  
Jia Lei Xiao ◽  
Bi Xian Zhang ◽  
Hong Tao Li ◽  
...  
Keyword(s):  
Fungal Community ◽  
18S Rdna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Limited Information ◽  
Rdna Sequences ◽  
Microbiological Techniques ◽  
Gradient Gel Electrophoresis ◽  
Realistic View ◽  
Specific Amplification

Like bacteria, fungi play an important role in the composting process as major decomposers of organic substances. As only a small fraction of the fungi present in composting can be cultured because conventional microbiological techniques limited information on the composition of fungal communities in composting. Molecular methods are expected to give a more realistic view of species richness and distribution. For this purpose, we selected universal PCR primer set that allow the specific amplification of fungal 18S-ribosomal-DNA (rDNA) sequences. DNA was extracted from composting samples, and 18S rDNA genes were amplified by EF4/Fung5 (0.6kb) and EF4/NS2-GC (0.4kb). DGGE analysis of the fungal community in the composting of a microcosm experiment was carried out after amplification of total DNA with both primer pairs. Clear banding patterns were obtained with amplified production. 13 different bands excised from the DGGE gel were sequenced and compared with genbank. Sequencing showed that some could not be cultured; some were efficient cellulose-degrading strains. The results showed that diversity and composition of the fungal community in the composting can be analyzed by the combination of 18S rDNA PCR amplification and DGGE.

scholarly journals Characterization of a Novel Spirochete Associated with the Hydrothermal Vent Polychaete Annelid, Alvinella pompejana

2001 ◽  
Vol 67 (1) ◽  
pp. 110-117 ◽  
Author(s):  
Barbara J. Campbell ◽  
S. Craig Cary
Keyword(s):  
High Temperature ◽  
Hydrothermal Vent ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Dorsal Surface ◽  
Specific Primers ◽  
Gradient Gel Electrophoresis ◽  
Polychaetous Annelid ◽  
Alvinella Pompejana

ABSTRACT A highly integrated, morphologically diverse bacterial community is associated with the dorsal surface of Alvinella pompejana, a polychaetous annelid that inhabits active high-temperature deep-sea hydrothermal vent sites along the East Pacific Rise (EPR). Analysis of a previously prepared bacterial 16S ribosomal DNA (rDNA) library identified a spirochete most closely related to an endosymbiont of the oligochete Olavius loisae. This spirochete phylotype (spirochete A) comprised only 2.2% of the 16S rDNA clone library but appeared to be much more dominant when the same sample was analyzed by denaturing gradient gel electrophoresis (DGGE) and the terminal restriction fragment length polymorphism procedure (12 to 18%). PCR amplification of the community with spirochete-specific primers used in conjunction with DGGE analysis identified two spirochete phylotypes. The first spirochete was identical to spirochete A but was present in only one A. pompejana specimen. The second spirochete (spirochete B) was 84.5% similar to spirochete A and, more interestingly, was present in the epibiont communities of all of theA. pompejana specimens sampled throughout the geographic range of the worm (13°N to 32°S along the EPR). The sequence variation of the spirochete B phylotype was less than 3% for the range of A. pompejana specimens tested, suggesting that a single spirochete species was present in the A. pompejanaepibiotic community. Additional analysis of the environments surrounding the worm revealed that spirochetes are a ubiquitous component of high-temperature vents and may play an important role in this unique ecosystem.

scholarly journals Direct Identification in Food Samples of Listeria spp. and Listeria monocytogenes by Molecular Methods

2002 ◽  
Vol 68 (12) ◽  
pp. 6273-6282 ◽  
Author(s):  
Luca Cocolin ◽  
Kalliopi Rantsiou ◽  
Lucilla Iacumin ◽  
Carlo Cantoni ◽  
Giuseppe Comi
Keyword(s):  
Listeria Monocytogenes ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Direct Detection ◽  
Pcr Amplification ◽  
Food Samples ◽  
Detection And Identification ◽  
Optimized Protocol ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
Species Specific

ABSTRACT A new molecular approach for the detection and identification of Listeria spp. and Listeria monocytogenes in food is presented here. The method is based on the PCR amplification of a fragment of the iap gene from the five species belonging to the genus and on the analysis of the PCR products obtained by denaturing gradient gel electrophoresis (DGGE). The protocol was first optimized by using strains from international collections. Based on the differences present in the sequences amplified, it was possible to obtain species-specific DGGE migration that allowed fast and easy identification of L. monocytogenes, L. innocua, L. welshimeri, L. seeligeri, and L. ivanovii. Moreover, for L. monocytogenes serotypes, partial differentiation was possible. The optimized protocol was used for identification of Listeria strains traditionally isolated from food and for direct detection and identification of Listeria members in food after an overnight enrichment. Identification of 48 food isolates and direct detection of Listeria spp. in 73 food samples show the potential of the method that can be used as a fast screening test to investigate the presence of Listeria spp. and L. monocytogenes in food.

Bioleaching of a Zinc Sulfide Ore by Thermophilic Consortia Isolated from Copahue Volcano

2007 ◽  
Vol 20-21 ◽  
pp. 79-82 ◽  
Author(s):  
Alejandra Giaveno ◽  
Edgardo R. Donati
Keyword(s):  
16S Rdna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Thermophilic Bacteria ◽  
Pcr Amplification ◽  
Zinc Recovery ◽  
The North ◽  
Sulfide Ore ◽  
Gradient Gel Electrophoresis ◽  
Shake Flasks ◽  
The Media

Bioleaching of a sulfide ore was investigated using a consortium of thermophilic bacteria and archaea. The consortium was obtained through successive enrichment procedures (using M88 with tetrathionate) after isolating from two different places into the geothermal area (Baño 9 and Las Maquinitas) of the Copahue volcano (in the north of Neuquén province in Argentina). Bioleaching experiments were carried out in 250-ml shake flasks with 100 ml of media and 1 g of the sulfide ore. Flasks were incubated at 150 rpm and 70 oC. The major constituents of the ore (La Resbalosa, Argentina) were sphalerite, pyrite, chalcopyrite and galena. The sample used throughout bioleaching experiments contained 22.5 % Zn. Two different media (0K and M88) were evaluated with and without the addition of elemental sulfur. Genetic diversity analysis of the microbial community was performed by PCR amplification of bacterial 16S rDNA fragments and analyzed by DGGE (denaturing gradient gel electrophoresis). The 16S rDNA was amplified by using eubacteria and archaea primers. Metal concentration, Eh and pH were periodically analyzed. Solid residues were filtered, washed, dried and finally analyzed by XRD and XRF. After 45 days, more than 50 % of zinc and about 100 % of the copper were solubilized. Galena and jarosite were detected in the solid residues. The data indicated that the dominant acidophiles were bacteria or archaea according to the media. M88 media allowed an important decrease of pH and higher zinc extractions while the presence of sulfur did not show significant influence on the zinc recovery.

scholarly journals Suicide Polymerase Endonuclease Restriction, a Novel Technique for Enhancing PCR Amplification of Minor DNA Templates

2005 ◽  
Vol 71 (8) ◽  
pp. 4721-4727 ◽  
Author(s):  
Stefan J. Green ◽  
Dror Minz
Keyword(s):  
16S Rrna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Environmental Dna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Dna Templates ◽  
Target Dna ◽  
Gradient Gel Electrophoresis ◽  
Pcr Method

ABSTRACT PCR-based molecular analyses can be hindered by the presence of unwanted or dominant DNA templates that reduce or eliminate detection of alternate templates. We describe here a reaction in which such templates can be exclusively digested by endonuclease restriction, leaving all other DNAs unmodified. After such a modification, the digested template is no longer available for PCR amplification, while nontarget DNAs remain intact and can be amplified. We demonstrate the application of this method and use denaturing gradient gel electrophoresis to ascertain the removal of target DNA templates and the subsequent enhanced amplification of nondigested DNAs. Specifically, plastid 16S rRNA genes were exclusively digested from environmental DNA extracted from plant roots. In addition, pure culture and environmental DNA extracts were spiked with various amounts of genomic DNA extracted from Streptomyces spp., and selective restriction of the Streptomyces 16S rRNA genes via the suicide polymerase endonuclease restriction PCR method was employed to remove the amended DNA.

scholarly journals Culture-Independent Analysis of Probiotic Products by Denaturing Gradient Gel Electrophoresis

2003 ◽  
Vol 69 (1) ◽  
pp. 220-226 ◽  
Author(s):  
R. Temmerman ◽  
I. Scheirlinck ◽  
G. Huys ◽  
J. Swings
Keyword(s):  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Human Consumption ◽  
Probiotic Potential ◽  
Conventional Culture ◽  
Freeze Dried ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Culture Dependent

ABSTRACT In order to obtain functional and safe probiotic products for human consumption, fast and reliable quality control of these products is crucial. Currently, analysis of most probiotics is still based on culture-dependent methods involving the use of specific isolation media and identification of a limited number of isolates, which makes this approach relatively insensitive, laborious, and time-consuming. In this study, a collection of 10 probiotic products, including four dairy products, one fruit drink, and five freeze-dried products, were subjected to microbial analysis by using a culture-independent approach, and the results were compared with the results of a conventional culture-dependent analysis. The culture-independent approach involved extraction of total bacterial DNA directly from the product, PCR amplification of the V3 region of the 16S ribosomal DNA, and separation of the amplicons on a denaturing gradient gel. Digital capturing and processing of denaturing gradient gel electrophoresis (DGGE) band patterns allowed direct identification of the amplicons at the species level. This whole culture-independent approach can be performed in less than 30 h. Compared with culture-dependent analysis, the DGGE approach was found to have a much higher sensitivity for detection of microbial strains in probiotic products in a fast, reliable, and reproducible manner. Unfortunately, as reported in previous studies in which the culture-dependent approach was used, a rather high percentage of probiotic products suffered from incorrect labeling and yielded low bacterial counts, which may decrease their probiotic potential.

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