Revealing Genetic Diversity of Eukaryotic Microorganisms in Aquatic Environments by Denaturing Gradient Gel Electrophoresis

Hannen, Erik J. van; Agterveld, Miranda P. van; Gons, Herman J.; Laanbroek, Hendrikus J.

doi:10.1046/j.1529-8817.1998.340206.x

Cited by 114 publications

(89 citation statements)

References 43 publications

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“…Amplification of the eukaryotic microorganisms in fish intestine was performed as described by Yu et al (2008) using 18S rRNA gene primers F1427 (5 -TCTGTGATG CCCTTAGATGTTCTGGG-3 with GC clamp in the 5 end) and R1616 (5 -GCGGTGTGTACAAAGGGCAGGG-3 ) (van Hannen et al, 1998). A 652 bp COI gene was amplified by the following primers: FishF1 (5 -TCAACCAACCACAAA GACATTGGCAC-3 ) and FishR1 (5 -TAGACTTCTGGG TGGCCAAAGAATCA-3 ) (Ward et al, 2005).…”

Section: Pcr Amplificationmentioning

confidence: 99%

Host species as a strong determinant of the intestinal microbiota of fish larvae

et al. 2012

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We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models. Results showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical.

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Section: Pcr Amplificationmentioning

confidence: 99%

Host species as a strong determinant of the intestinal microbiota of fish larvae

et al. 2012

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“…Finally, a primer extension at 72-C for 10 min was performed. The primers used for amplification of the 18S rRNA genes were F1427GC (5 0 -CGCC CGCCGCGCCCCGCGCCCGGCCCGCCGCCCCCGC CCCTCTGTGATGCCCTTAGATGTTCTGGG-3 0 ) and R1616 (5 0 -GCGGTGTGTACAAAGGGCAGGG-3 0 ) [21]. Both of them are specific to eukaryotic microorganisms.…”

Section: Study Sites and Sample Collectionmentioning

confidence: 99%

“…Yu et al [28] explored the feasibility of DNA fingerprinting to community-level analysis and Yan et al [27] applied random amplified polymorphic DNA (RAPD) to investigate DNA polymorphism of plankton communities. These DNA-based community-level studies, together with others, have significantly increased our understanding of community diversity [14,21,29], which, in turn, makes it possible to elucidate the manner in which molecular-level actions influence ecosystem changes. Among all of the available fingerprinting approaches, PCR-DGGE is one of the most commonly used methods to investigate the diversity and spatialtemporal dynamics of communities [26].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Plankton Community as Depicted by PCR-DGGE Fingerprinting and its Relation to Morphological Composition and Environmental Factors in Lake Donghu

et al. 2007

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To collect information about the genetic diversity of the plankton community and to study how plankton respond to environmental conditions, plankton samples were collected from five stations representing different trophic levels in a shallow, eutrophic lake (Lake Donghu), and investigated by PCR-DGGE fingerprinting. A total of 100 bands (61 of 16S rDNA bands and 39 of 18S rDNA bands) were detected. The DGGE bands unique to any single station accounted for 38% of the total bands, whereas common bands detected at all five stations accounted for only 11%. Using UPGMA clustering and MDS ordination of DGGE fingerprints, stations I and II were found to initially group together into one cluster, which was later joined by station V. Stations III and IV were isolated into two separate groups of one station each. Some differences in grouping relationships were found when analysis was completed on the basis of chemical characteristics and morphological composition, with zooplankton composition showing the greatest variability. However, the most similar stations (I and II) were always initially grouped into one cluster. Moreover, stations that exhibited the same or similar trophic level (stations III and IV), but different concentrations of heavy metals, were further differentiated by the DGGE method. Results of the present study indicated that PCR-DGGE fingerprinting was more sensitive than the traditional methods, as other studies suggested. Additionally, PCR-DGGE appears to be more appropriate for diversity characterization of the plankton community, as it is more canonical, systematic, and effective. Most importantly, fingerprinting results are more convenient for the comparative analyses between different studies. Therefore, the use of the described fingerprinting analysis may provide an operable and sensitive biomonitoring approach to identify critical, and potentially negative, stress within an aquatic ecosystem.

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“…Since then, DGGE has been widely used to study natural community composition in numerous environments (Muyzer and Smalla, 1998). Although the DGGE banding patterns (OTU composition) may not reflect the community a hundred percent, it has become a reliable and popular method for the examination of differences and similarities in community composition (van Hannen et al, 1998;Lindström, 2000).…”

Section: Introductionmentioning

confidence: 99%

“…DGGE analysis of 18S rRNA genes has also been applied to the exploration of the diversity of microbial eukaryotic communities (van Hannen et al, 1998;Savin et al, 2004). More recently, Yan et al (2007) explored the genetic diversity of both the bacterial and the eukaryotic plankton communities (with DGGE analysis of the 16S rDNA and 18S rDNA) in a shallow freshwater lake.…”

Section: Introductionmentioning

confidence: 99%

Plankton community composition in the Three Gorges Reservoir Region revealed by PCR-DGGE and its relationships with environmental factors

Yan

Feng

et al. 2008

Journal of Environmental Sciences

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Revealing Genetic Diversity of Eukaryotic Microorganisms in Aquatic Environments by Denaturing Gradient Gel Electrophoresis

Cited by 114 publications

References 43 publications

Host species as a strong determinant of the intestinal microbiota of fish larvae

Host species as a strong determinant of the intestinal microbiota of fish larvae

Genetic Diversity of Plankton Community as Depicted by PCR-DGGE Fingerprinting and its Relation to Morphological Composition and Environmental Factors in Lake Donghu

Plankton community composition in the Three Gorges Reservoir Region revealed by PCR-DGGE and its relationships with environmental factors

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