Denaturing gradient gel electrophoresis in marine microbial ecology

Schäfer, Hendrik; Muyzer, Gerard

doi:10.1016/s0580-9517(01)30057-0

Cited by 272 publications

(223 citation statements)

References 62 publications

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“…The nearly complete 16S rRNA gene was obtained from pure cultures using bacterial primers GM3F and GM4R (Schäfer and Muyzer 2001). The PCR products were purified from low-melting agarose using the Wizard PCR-Prep kit (Promega, USA) according to the manufacturer's instructions.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Influence of salts and pH on growth and activity of a novel facultatively alkaliphilic, extremely salt-tolerant, obligately chemolithoautotrophic sufur-oxidizing Gammaproteobacterium Thioalkalibacter halophilus gen. nov., sp. nov. from South-Western Siberian soda lakes

et al. 2008

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Section: Phylogenetic Analysismentioning

confidence: 99%

Influence of salts and pH on growth and activity of a novel facultatively alkaliphilic, extremely salt-tolerant, obligately chemolithoautotrophic sufur-oxidizing Gammaproteobacterium Thioalkalibacter halophilus gen. nov., sp. nov. from South-Western Siberian soda lakes

et al. 2008

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“…Denaturing gradient gel electrophoresis (DGGE) was performed as described by Schäfer & Muyzer [25]. Briefly, 1-mm thick 6% acrylamide gels with a urea-formamide gradient of 20-80% were used for bacterial 16S rRNA gene fragments.…”

Section: Dna Extractionmentioning

confidence: 99%

Heterotrophic Pioneers Facilitate Phototrophic Biofilm Development

2007

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Phototrophic biofilms are matrix-enclosed microbial communities, mainly driven by light energy. In this study, the successional changes in community composition of freshwater phototrophic biofilms growing on polycarbonate slides under different light intensities were investigated. The sequential changes in community composition during different developmental stages were examined by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments in conjugation with sequencing and phylogenetic analysis. Biofilm development was monitored with subsurface light sensors. The development of these biofilms was clearly light dependent. It was shown that under high light conditions the initial colonizers of the substratum predominantly consisted of green algae, whereas at low light intensities, heterotrophic bacteria were the initial colonizers. Cluster analysis of DGGE banding patterns revealed a clear correlation in the community structure with the developmental phases of the biofilms. At all light intensities, filamentous cyanobacteria affiliated to Microcoleus vaginatus became dominant as the biofilms matured. It was shown that the initial colonization phase of the phototrophic biofilms is shorter on polycarbonate surfaces precolonized by heterotrophic bacteria.

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“…Denaturing gradient gel electrophoresis (DGGE) has been used extensively for examination of complex microbial community assemblages (6,20,30,46,52). DGGE analyses are influenced by methodological limitations, as with any PCR-based approach (55), and the prevalent consensus is that major populations are reflected in the molecular fingerprint of an environmental sample (38,41). Nevertheless, Fromin et al (16) suggest that possible biases in DNA extraction and amplification become homogenous if identical methods are used to process samples, which are then subjected to DGGE analysis.…”

mentioning

confidence: 99%

Diversity of Fungi, Bacteria, and Actinomycetes on Leaves Decomposing in a Stream

Das

Royer

Leff

2007

Appl Environ Microbiol

191

137

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Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCRdenaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycetespecific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality.

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Denaturing gradient gel electrophoresis in marine microbial ecology

Cited by 272 publications

References 62 publications

Influence of salts and pH on growth and activity of a novel facultatively alkaliphilic, extremely salt-tolerant, obligately chemolithoautotrophic sufur-oxidizing Gammaproteobacterium Thioalkalibacter halophilus gen. nov., sp. nov. from South-Western Siberian soda lakes

Influence of salts and pH on growth and activity of a novel facultatively alkaliphilic, extremely salt-tolerant, obligately chemolithoautotrophic sufur-oxidizing Gammaproteobacterium Thioalkalibacter halophilus gen. nov., sp. nov. from South-Western Siberian soda lakes

Heterotrophic Pioneers Facilitate Phototrophic Biofilm Development

Diversity of Fungi, Bacteria, and Actinomycetes on Leaves Decomposing in a Stream

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