scholarly journals Biodiversity of Thermophilic Prokaryotes with Hydrolytic Activities in Hot Springs of Uzon Caldera, Kamchatka (Russia)

2008 ◽  
Vol 75 (1) ◽  
pp. 286-291 ◽  
Author(s):  
Ilya V. Kublanov ◽  
Anna A. Perevalova ◽  
Galina B. Slobodkina ◽  
Aleksander V. Lebedinsky ◽  
Salima K. Bidzhieva ◽  
...  
Keyword(s):  
Hot Springs ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Specific Primers ◽  
Uzon Caldera ◽  
Dgge Analysis ◽  
Hydrolytic Activities ◽  
Gradient Gel Electrophoresis ◽  
Polymeric Substrates

ABSTRACT Samples of water from the hot springs of Uzon Caldera with temperatures from 68 to 87�C and pHs of 4.1 to 7.0, supplemented with proteinaceous (albumin, casein, or α- or β-keratin) or carbohydrate (cellulose, carboxymethyl cellulose, chitin, or agarose) biological polymers, were filled with thermal water and incubated at the same sites, with the contents of the tubes freely accessible to the hydrothermal fluid. As a result, several enrichment cultures growing in situ on different polymeric substrates were obtained. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments obtained after PCR with Bacteria-specific primers showed that the bacterial communities developing on carbohydrates included the genera Caldicellulosiruptor and Dictyoglomus and that those developing on proteins contained members of the Thermotogales order. DGGE analysis performed after PCR with Archaea- and Crenarchaeota-specific primers showed that archaea related to uncultured environmental clones, particularly those of the Crenarchaeota phylum, were present in both carbohydrate- and protein-degrading communities. Five isolates obtained from in situ enrichments or corresponding natural samples of water and sediments represented the bacterial genera Dictyoglomus and Caldanaerobacter as well as new archaea of the Crenarchaeota phylum. Thus, in situ enrichment and consequent isolation showed the diversity of thermophilic prokaryotes competing for biopolymers in microbial communities of terrestrial hot springs.

scholarly journals Molecular Characterization of Community Structures and Sulfur Metabolism within Microbial Streamers in Japanese Hot Springs

2003 ◽  
Vol 69 (12) ◽  
pp. 7044-7057 ◽  
Author(s):  
Tatsunori Nakagawa ◽  
Manabu Fukui
Keyword(s):  
Hot Springs ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Sulfur Metabolism ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Community Structures ◽  
Rt Pcr ◽  
Sulfide Production ◽  
Gradient Gel Electrophoresis

ABSTRACT Community structures of submerged microbial slime streamers (SMSS) in sulfide-containing hot springs at 72 to 80°C at Nakabusa and Yumata, Japan, were investigated by molecular analysis based on the 16S rRNA gene. The SMSS were classified into two consortia; consortium I occurred at lower levels of sulfide in the hot springs (less than 0.1 mM), and consortium II dominated when the sulfide levels were higher (more than 0.1 mM). The dominant cell morphotypes in consortium I were filamentous and small rod-shaped cells. The filamentous cells hybridized with fluorescent oligonucleotide probes for the domain Bacteria, the domain Archaea, and the family Aquificaceae. Our analysis of the denaturing gradient gel electrophoresis (DGGE) bands by using reverse transcription (RT)-PCR amplification with two primer sets (Eub341-F with the GC clamp and Univ907R for the Bacteria and Eub341-F with the GC clamp and Arch915R) indicated that dominant bands were phylogenetically related to microbes in the genus Aquifex. On the other hand, consortium II was dominated by long, small, rod-shaped cells, which hybridized with the oligonucleotide probe S-*-Tdes-0830-a-A-20 developed in this study for the majority of as-yet-uncultivated microbes in the class Thermodesulfobacteria. The dominant DGGE band obtained by PCR and RT-PCR was affiliated with the genus Sulfurihydrogenibium. Moreover, our analysis of dissimilatory sulfite reductase (DSR) gene sequences retrieved from both consortia revealed a high frequency of DSR genes corresponding to the DSR of Thermodesulfobacteria-like microorganisms. Using both sulfide monitoring and 35SO4 2− tracer experiments, we observed microbial sulfide production and consumption by SMSS, suggesting that there is in situ sulfide production by as-yet-uncultivated Thermodesulfobacteria-like microbes and there is in situ sulfide consumption by Sulfurihydrogenibium-like microbes within the SMSS in the Nakabusa and Yumata hot springs.

scholarly journals Characterization of a Culturable Alphaproteobacterial Symbiont Common to Many Marine Sponges and Evidence for Vertical Transmission via Sponge Larvae

2006 ◽  
Vol 72 (5) ◽  
pp. 3724-3732 ◽  
Author(s):  
Julie J. Enticknap ◽  
Michelle Kelly ◽  
Olivier Peraud ◽  
Russell T. Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Marine Sponges ◽  
Rrna Gene ◽  
Surrounding Water ◽  
Axinella Corrugata ◽  
Gradient Gel Electrophoresis ◽  
Related Group

ABSTRACT A closely related group of alphaproteobacteria were found to be present in seven genera of marine sponges from several locations and were shown to be transferred between sponge generations through the larvae in one of these sponges. Isolates of the alphaproteobacterium were cultured from the sponges Axinella corrugata, Mycale laxissima, Monanchora unguifera, and Niphates digitalis from Key Largo, Florida; Didiscus oxeata and Monanchora unguifera from Discovery Bay, Jamaica; an Acanthostronglyophora sp. from Manado, Indonesia; and Microciona prolifera from the Cheasapeake Bay in Maryland. Isolates were very similar to each other on the basis of 16S rRNA gene sequence (>99% identity) and are closely related to Pseudovibrio denitrificans. The bacterium was never isolated from surrounding water samples and was cultured from larvae of M. laxissima, indicating that it is a vertically transmitted symbiont in this sponge. Denaturing gradient gel electrophoresis, 16S rRNA gene clone library analysis, and fluorescent in situ hybridization with probes specific to the alphaproteobacterium confirmed the presence of this bacterium in the M. laxissima larvae. The alphaproteobacterium was densely associated with the larvae rather than being evenly distributed throughout the mesohyl. This is the first report of the successful culture of a bacterial symbiont of a sponge that is transferred through the gametes.

PCR-DGGE Analysis of Bacterial Diversity of Intestinal System in Hyperlipidemia Rats

2013 ◽  
Vol 726-731 ◽  
pp. 898-901
Author(s):  
Ri Na Wu ◽  
Xiao Meng Pang ◽  
Xi Yan Wang ◽  
Jun Rui Wu
Keyword(s):  
Bacterial Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Intestinal Flora ◽  
Intestinal Bacteria ◽  
Control Group ◽  
Rrna Gene ◽  
Dgge Analysis ◽  
Gradient Gel Electrophoresis ◽  
The Relationship ◽  
Insight Into

Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene has been regarded as one of powerful tools for gaining insight into the bacterial diversity of intestinal system. In the present study, hyperlipidemia model was constructed in rat according to the tests of blood lipids. Fecal samples of rats were collected after 60d feeding, and DGGE was used to investigate the diversities of intestinal bacteria in the artificially-induced hyperlipidemia rats and normal rats. The results showed that two patterns had similarities, but there were also some different bacteria communities. Moreover, control group had much more bands than model group on gel, showing species in intestinal of model rats might be deduced by hyperlipidemia. It will be helpful to explore the relationship between hyperlipidemia and intestinal flora.

Composition of the bacterial biota in slime developed in two machines at a Canadian paper mill

2011 ◽  
Vol 57 (2) ◽  
pp. 91-104 ◽  
Author(s):  
Julie Disnard ◽  
Carole Beaulieu ◽  
Richard Villemur
Keyword(s):  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Paper Mill ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Paper Machines ◽  
Gradient Gel Electrophoresis ◽  
Candidate Division ◽  
Catalyzed Reporter Deposition

During the process of papermaking by pulp and paper plants, a thick and viscous deposits, termed slime, is quickly formed around the paper machines, which can affect the papermaking process. In this study, we explored the composition of the bacterial biota in slime that developed on shower pipes from 2 machines at a Canadian paper mill. Firstly, the composition was assessed for 12 months by DNA profiling with polymerase chain reaction coupled with denaturing gradient gel electrophoresis. Except for short periods (2–3 months), clustered analyses showed that the bacterial composition of the slime varied substantially over the year, with less than 50% similarity between the denaturing gradient gel electrophoresis profiles. Secondly, the screening of 16S rRNA gene libraries derived from 2 slime samples showed that the most abundant bacteria were related to 6 lineages, including Chloroflexi, candidate division OP10, Clostridiales, Bacillales, Burkholderiales, and the genus Deinococcus . Finally, the proportion of 8 bacterial lineages, such as Deinococcus sp., Meiothermus sp., and Chloroflexi, was determined by the Catalyzed Reporter Deposition – Fluorescence In Situ Hybridization in 2 slime samples. The results showed a high proportion of Chloroflexi, Tepidimonas spp., and Schlegelella spp. in the slime samples.

Denaturing Gradient Gel Electrophoresis Detects Bacterial and Cyaonbacterial Diversities in Biological Soil Crusts in a Semiarid Desert, China

2013 ◽  
Vol 726-731 ◽  
pp. 3680-3684
Author(s):  
Ying Zhang ◽  
Cheng You Cao ◽  
Peng Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Biological Soil Crusts ◽  
Rrna Gene ◽  
Sandy Land ◽  
Specific Primers ◽  
Soil Crusts ◽  
Gradient Gel Electrophoresis

The purpose of this study is to assess the application of denaturing gradient gel electrophoresis (DGGE) for analyzing the bacterial and cyanobacterial diversities of biological soil crusts (BSCs) in sandy land. Soil microbial DNA was extracted from BSCs under different plantations in Horqin Sandy Land of Northeast China. 16S rRNA gene fragments from bacteria and cyanobacteria were amplified by universal bacterial and cyanobacteria-specific primers. Fourteen and six prominent bands were detected in the bacterial and cyanobacterial DGGE profiles, respectively. These bands were excised, cloned and sequenced. Phylogenetic analysis classified the bacterial sequences into the following main groups:Escherichia,Bacillus,Paenibacillus,Shigella, andPseudomonas. The cyanobacterial sequences were classified asMicrocoleus,LeptolyngbyaandHaslea. Our study suggests that DGGE is a useful technique for detecting dominant species compositions of bacterial and cyanobacterial communities in biological soil crusts, and specific primers are recommended for PCR of 16S rRNA gene fragments.

scholarly journals Characterization of the bacterial community structure of Sydney Tar Ponds sediment

2011 ◽  
Vol 57 (6) ◽  
pp. 493-503 ◽  
Author(s):  
C. William Yeung ◽  
Monica Woo ◽  
Kenneth Lee ◽  
Charles W. Greer
Keyword(s):  
Clone Library ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Toxic Waste ◽  
Rrna Gene ◽  
Dgge Analysis ◽  
Gradient Gel Electrophoresis ◽  
Primer Sets ◽  
V3 Region ◽  
Mycobacterium Spp

The Sydney Tar Ponds is one of the largest toxic waste sites in Canada. The bacterial diversity and abundance in the Sydney Tar Ponds sediment was examined using a 16S rRNA gene clone library and denaturing gradient gel electrophoresis (DGGE) with four different primer sets. The clone library was grouped into 19 phylotypes that could be divided into five phyla: Proteobacteria (56.9%), Actinobacteria (35%), Acidobacteria (4.9%), Firmicutes (2.4%), and Verrucomicrobia (0.8%). Members of the phyla Actinobacteria (represented mainly by Mycobacterium spp.) and Alphaproteobacteria (represented by Acidocella spp.) comprised the majority of the clone library. This study also revealed that the phylogenetic results obtained from clone library analysis and from DGGE analysis, with all the primer sets, showed some variability. However, similar Mycobacterium spp. and Acidocella spp. were found in all the different DGGE analyses, again suggesting that these two genera are dominant in the Sydney Tar Ponds sediment. In addition, DGGE analysis indicated that primer sets targeting the V3 region produced results that were the most similar to those obtained with the clone library.

scholarly journals Novel Epibiotic Thiothrix Bacterium on a Marine Amphipod

2004 ◽  
Vol 70 (6) ◽  
pp. 3772-3775 ◽  
Author(s):  
David C. Gillan ◽  
Nicole Dubilier
Keyword(s):  
Gel Electrophoresis ◽  
Fluorescent In Situ Hybridization ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Filamentous Bacteria ◽  
Gradient Gel Electrophoresis ◽  
Marine Amphipod ◽  
Amphipod Crustacean ◽  
The 16S Rrna Gene

ABSTRACT Comparative analysis of the 16S rRNA gene and fluorescent in situ hybridization (FISH) was used to identify epibiotic filamentous bacteria living on the marine amphipod crustacean Urothoe poseidonis. The epibionts belong to the gamma proteobacteria and represent a novel marine phylotype within the genus Thiothrix. FISH and denaturing gradient gel electrophoresis revealed that the Thiothrix filaments are present on the majority of the amphipods examined.

scholarly journals Differences between Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and Its Mounds

2007 ◽  
Vol 73 (16) ◽  
pp. 5199-5208 ◽  
Author(s):  
Saliou Fall ◽  
Jérôme Hamelin ◽  
Farma Ndiaye ◽  
Komi Assigbetse ◽  
Michel Aragno ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Termite Mound ◽  
Dgge Analysis ◽  
Termite Gut ◽  
Gradient Gel Electrophoresis ◽  
High Level ◽  
Surrounding Soil

ABSTRACT In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.

scholarly journals Development and Validation of a Nested-PCR-Denaturing Gradient Gel Electrophoresis Method for Taxonomic Characterization of Bifidobacterial Communities

2003 ◽  
Vol 69 (11) ◽  
pp. 6380-6385 ◽  
Author(s):  
R. Temmerman ◽  
L. Masco ◽  
T. Vanhoutte ◽  
G. Huys ◽  
J. Swings
Keyword(s):  
Nested Pcr ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Temporal Changes ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Gradient Gel Electrophoresis ◽  
Species Specific ◽  
Taxonomic Characterization

ABSTRACT The taxonomic characterization of a bacterial community is difficult to combine with the monitoring of its temporal changes. None of the currently available identification techniques are able to visualize a “complete” community, whereas techniques designed for analyzing bacterial ecosystems generally display limited or labor-intensive identification potential. This paper describes the optimization and validation of a nested-PCR-denaturing gradient gel electrophoresis (DGGE) approach for the species-specific analysis of bifidobacterial communities from any ecosystem. The method comprises a Bifidobacterium-specific PCR step, followed by purification of the amplicons that serve as template DNA in a second PCR step that amplifies the V3 and V6-V8 regions of the 16S rRNA gene. A mix of both amplicons is analyzed on a DGGE gel, after which the band positions are compared with a previously constructed database of reference strains. The method was validated through the analysis of four artificial mixtures, mimicking the possible bifidobacterial microbiota of the human and chicken intestine, a rumen, and the environment, and of two fecal samples. Except for the species Bifidobacterium coryneforme and B. indicum, all currently known bifidobacteria originating from various ecosystems can be identified in a highly reproducible manner. Because no further cloning and sequencing of the DGGE bands is necessary, this nested-PCR-DGGE technique can be completed within a 24-h span, allowing the species-specific monitoring of temporal changes in the bifidobacterial community.

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