scholarly journals   Effect of legume-cereal mixtures on the diversity of bacterial communities in the rhizosphere

2012 ◽  
Vol 58 (No. 4) ◽  
pp. 174-180 ◽  
Author(s):  
Y.J. Qiao ◽  
Z.H. Li ◽  
X. Wang ◽  
B. Zhu ◽  
Y.G. Hu ◽  
...  
Keyword(s):  
16S Rdna ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Cropping Systems ◽  
Microbial Succession ◽  
Common Vetch ◽  
Soil Microbial ◽  
Rdna Sequences ◽  
Gradient Gel Electrophoresis ◽  
Belowground Diversity

Aboveground plant diversity is known to influence belowground diversity and ecosystem processes. However, there is little knowledge of soil microbial succession in legume-grass mixtures. Therefore, this study was designed to determine the effect of oat and common vetch binary mixtures at three seeding rates on soil bacterial communities. Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA fragments was used to profile the structure of the bacterial community in the rhizosphere. Compared with a monoculture of common vetch and oat, the Shannon-Weaver index and species richness of the mixtures were increased. Thirteen cloned monocultures and mixtures of oat and common vetch soil 16S rDNA sequences were deposited to NCBI. Based on the sequencing results, the bands could be identified as related to Proteobacteria, Bacteroidetes and Cyanobacteria. Common vetch did not have some bacteria relatives to Sphingomonas spp. Some bacterial taxa could be detected in the ratio of 1:1 and 1:2, but not in the ratio of 1:3, e.g. Myxococcales. The results suggested that the belowground diversity could be promoted by mixed cropping systems.  

scholarly journals Molecular Monitoring of Succession of Bacterial Communities in Human Neonates

2002 ◽  
Vol 68 (1) ◽  
pp. 219-226 ◽  
Author(s):  
Christine F. Favier ◽  
Elaine E. Vaughan ◽  
Willem M. De Vos ◽  
Antoon D. L. Akkermans
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Colonization ◽  
Molecular Monitoring ◽  
Fecal Samples ◽  
16S Rdna Sequence Analysis ◽  
Rdna Sequences ◽  
Gradient Gel Electrophoresis

ABSTRACT The establishment of bacterial communities in two healthy babies was examined for more than the first 10 months of life by monitoring 16S ribosomal DNA (rDNA) diversity in fecal samples by PCR and denaturing gradient gel electrophoresis (DGGE) and by analyzing the sequences of the major ribotypes. DGGE profiles of the dominant populations in the intestines of the infants were obtained by analyzing daily or weekly fecal samples. After delivery, the germfree infant gastrointestinal tracts were rapidly colonized, and the succession of bacteria in each ecosystem was monitored. During the first few days of life the profiles were simple, but they became more complex as the bacterial diversity increased with time in both babies. Clone libraries of amplified 16S rDNA fragments from baby feces were constructed, and these libraries allowed identification of the bacterial types by comparative DNA sequence analysis; the bacteria identified included members of the genera Bifidobacterium, Ruminococcus, Enterococcus, Clostridium, and Enterobacter. Species most closely related to the genera Bifidobacterium and Ruminococcus in particular dominated the intestinal microbiota based on the stability over time and the numbers, as estimated by the intensities of the bands. However, 19 of the 34 cloned rDNA sequences exhibited less than 97% identity with sequences of known bacteria or cloned sequences in databases. This study showed that using PCR-DGGE and 16S rDNA sequence analysis together resulted in a dynamic description of bacterial colonization in the infant intestinal ecosystem and allowed visualization of bacteria that are difficult to cultivate or to detect by other methods.

scholarly journals Bifidobacterial Diversity in Human Feces Detected by Genus-Specific PCR and Denaturing Gradient Gel Electrophoresis

2001 ◽  
Vol 67 (2) ◽  
pp. 504-513 ◽  
Author(s):  
Reetta M. Satokari ◽  
Elaine E. Vaughan ◽  
Antoon D. L. Akkermans ◽  
Maria Saarela ◽  
Willem M. de Vos
Keyword(s):  
16S Rdna ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Methodological Approach ◽  
Common Species ◽  
Bifidobacterium Adolescentis ◽  
Specific Pcr ◽  
Rdna Sequences ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis

ABSTRACT We describe the development and validation of a method for the qualitative analysis of complex bifidobacterial communities based on PCR and denaturing gradient gel electrophoresis (DGGE).Bifidobacterium genus-specific primers were used to amplify an approximately 520-bp fragment from the 16S ribosomal DNA (rDNA), and the fragments were separated in a sequence-specific manner in DGGE. PCR products of the same length from different bifidobacterial species showed good separation upon DGGE. DGGE of fecal 16S rDNA amplicons from five adult individuals showed host-specific populations of bifidobacteria that were stable over a period of 4 weeks. Sequencing of fecal amplicons resulted in Bifidobacterium-like sequences, confirming that the profiles indeed represent the bifidobacterial population of feces. Bifidobacterium adolescentis was found to be the most common species in feces of the human adult subjects in this study. The methodological approach revealed intragenomic 16S rDNA heterogeneity in the type strain of B. adolescentis, E-981074. The strain was found to harbor five copies of 16S rDNA, two of which were sequenced. The two 16S rDNA sequences of B. adolescentis E-981074T exhibited microheterogeneity differing in eight positions over almost the total length of the gene.

scholarly journals Denaturing gradient gel electrophoresis and multi-SIR profiles of soil microbial communities from a karst doline at Aggtelek National Park, Hungary

2020 ◽  
Author(s):  
Márton Mucsi ◽  
Gergely Krett ◽  
Tibor Szili-Kovács ◽  
János Móga ◽  
Andrea K. Borsodi
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Vegetation Type ◽  
Carbon Sources ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Soil Microbial ◽  
Gradient Gel Electrophoresis

Abstract Soils play an important role in the ecosystem of karstic landscapes both as a buffer zone and as a source of acidity to belowground water. Although the microbiota of karstic soils is known to have a great effect on karstification processes, the activity and composition of these communities are largely unknown. This study gives a comparative analysis of soil microbial profiles from different parts of a doline located at Aggtelek, Hungary. The aim was to reveal the relationships between the vegetation type and genetic fingerprints and substrate utilisation (multi-SIR) profiles of the soil microbiota. Soil samples were collected in early and late springs along a transect in a doline covered with different types of vegetation. Genetic fingerprints of bacterial communities were examined by denaturing gradient gel electrophoresis (DGGE) based on the 16S rRNA gene, along with multi-SIR profiles of the microbial communities measured by the MicroResp method using 15 different carbon sources. Genetic fingerprinting indicated that vegetation cover had a strong effect on the composition of soil bacterial communities. Procrustean analysis showed only a weak connection between DGGE and multi-SIR profiles, probably due to the high functional redundancy of the communities. Seasonality had a significant effect on substrate usage, which can be an important factor to consider in future studies.

scholarly journals Identification of a Bacterium That Specifically Catalyzes the Reductive Dechlorination of Polychlorinated Biphenyls with Doubly Flanked Chlorines

2002 ◽  
Vol 68 (2) ◽  
pp. 807-812 ◽  
Author(s):  
Qingzhong Wu ◽  
Joy E. M. Watts ◽  
Kevin R. Sowers ◽  
Harold D. May
Keyword(s):  
Polychlorinated Biphenyls ◽  
16S Rdna ◽  
Reductive Dechlorination ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rdna Sequence ◽  
16S Rdna Sequence ◽  
Sulfate Reducing ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
Gradient Gel Electrophoresis

ABSTRACT A microorganism whose growth is linked to the dechlorination of polychlorinated biphenyls (PCBs) with doubly flanked chlorines was identified. Identification was made by reductive analysis of community 16S ribosomal DNA (rDNA) sequences from a culture enriched in the presence of 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB), which was dechlorinated at the para position. Denaturing gradient gel electrophoresis (DGGE) analysis of total 16S rDNA extracted from the culture led to identification of three operational taxonomic units (OTUs 1, 2, and 3). OTU 1 was always detected when 2,3,4,5-CB or other congeners with doubly flanked chlorines were present and dechlorinated. Only OTUs 2 and 3 were detected in the absence of PCBs and when other PCBs (i.e., PCBs lacking doubly flanked chlorines) were not dechlorinated. Partial sequences of OTUs 2 and 3 exhibited 98.2% similarity to the sequence of “Desulfovibrio caledoniensis” (accession no. DCU53465 ). A sulfate-reducing vibrio isolated from the culture generated OTUs 2 and 3. This organism could not dechlorinate 2,3,4,5-CB. From these results we concluded that OTU 1 represents the dechlorinating bacterium growing in a coculture with a Desulfovibrio sp. The 16S rDNA sequence of OTU 1 is most similar to the 16S rDNA sequence of bacterium o-17 (89% similarity), an ortho-PCB-dechlorinating bacterium. The PCB dechlorinator, designated bacterium DF-1, reductively dechlorinates congeners with doubly flanked chlorines when it is supplied with formate or H2-CO2 (80:20).

Analysis of endophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis (DGGE) of 16S rDNA based PCR fragments

2001 ◽  
Vol 41 (4) ◽  
pp. 369-383 ◽  
Author(s):  
P. Garbeva ◽  
L. S. van Overbeek ◽  
J. W. L. van Vuurde ◽  
J. D. van Elsas
Keyword(s):  
16S Rdna ◽  
Bacterial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Gradient Gel Electrophoresis

scholarly journals Impact of Intensive Land-Based Fish Culture in Qingdao, China, on the Bacterial Communities in Surrounding Marine Waters and Sediments

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Qiufen Li ◽  
Yan Zhang ◽  
David Juck ◽  
Nathalie Fortin ◽  
Charles W. Greer
Keyword(s):  
Bacterial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Fish Culture ◽  
Fish Ponds ◽  
Marine Area ◽  
Gradient Gel Electrophoresis ◽  
Reducing Bacteria ◽  
The Impact ◽  
Nitrate Reducing Bacteria

The impact of intensive land-based fish culture in Qingdao, China, on the bacterial communities in surrounding marine environment was analyzed. Culture-based studies showed that the highest counts of heterotrophic, ammonium-oxidizing, nitrifying, and nitrate-reducing bacteria were found in fish ponds and the effluent channel, with lower counts in the adjacent marine area and the lowest counts in the samples taken from 500 m off the effluent channel. Denaturing gradient gel electrophoresis (DGGE) analysis was used to assess total bacterial diversity. Fewer bands were observed from the samples taken from near the effluent channel compared with more distant sediment samples, suggesting that excess nutrients from the aquaculture facility may be reducing the diversity of bacterial communities in nearby sediments. Phylogenetic analysis of the sequenced DGGE bands indicated that the bacteria community of fish-culture-associated environments was mainly composed of Flavobacteriaceae, gamma- and deltaproteobacteria, including generaGelidibacter, Psychroserpen, Lacinutrix,andCroceimarina.

scholarly journals Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities

2009 ◽  
Vol 55 (No. 10) ◽  
pp. 413-423 ◽  
Author(s):  
V. Valášková ◽  
P. Baldrian
Keyword(s):  
Microbial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Genes Encoding ◽  
Gradient Gel Electrophoresis ◽  
Temperature Gradient Gel Electrophoresis ◽  
Experimental Treatments ◽  
Multiple Samples

In soil microbial ecology, the effects of environmental factors and their gradients, temporal changes or the response to specific experimental treatments of microbial communities can only be effectively analyzed using methods that address the structural differences among whole communities. Fingerprinting methods are the most appropriate technique for this task when multiple samples must be analyzed. Among the methods currently used to compare microbial communities based on nucleic acid sequences, the techniques based on differences in the melting properties of double-stranded molecules, denaturing gradient gel electrophoresis (DGGE) or temperature gradient gel electrophoresis (TGGE), are the most widely used. Their main advantage is that they provide the possibility to further analyze whole sequences contained in fingerprints using molecular methods. In addition to the analysis of microbial communities based on DNA extracted from soils, DGGE/TGGE can also be used for the assessment of the active part of the community based on the analysis of RNA-derived sequences or for the analysis of sequences of functional genes encoding for proteins involved in important soil processes.

Profiling of Bacterial Species Associated with Haddock Larviculture by PCR Amplification of 16S rDNA and Denaturing Gradient Gel Electrophoresis

2001 ◽  
Vol 13 (4) ◽  
pp. 355-363 ◽  
Author(s):  
Steve Griffiths ◽  
Krista Melville ◽  
Marcia Cook ◽  
Sherry Vincent ◽  
Maurice Pierre ◽  
...  
Keyword(s):  
16S Rdna ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Pcr Amplification ◽  
Gradient Gel Electrophoresis
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