Dataset Information

An Improved DNA Extraction Method for Efficient and Quantitative Recovery of Phytoplankton Diversity in Natural Assemblages.

ABSTRACT: Marine phytoplankton are highly diverse with different species possessing different cell coverings, posing challenges for thoroughly breaking the cells in DNA extraction yet preserving DNA integrity. While quantitative molecular techniques have been increasingly used in phytoplankton research, an effective and simple method broadly applicable to different lineages and natural assemblages is still lacking. In this study, we developed a bead-beating protocol based on our previous experience and tested it against 9 species of phytoplankton representing different lineages and different cell covering rigidities. We found the bead-beating method enhanced the final yield of DNA (highest as 2 folds) in comparison with the non-bead-beating method, while also preserving the DNA integrity. When our method was applied to a field sample collected at a subtropical bay located in Xiamen, China, the resultant ITS clone library revealed a highly diverse assemblage of phytoplankton and other micro-eukaryotes, including Archaea, Amoebozoa, Chlorophyta, Ciliphora, Bacillariophyta, Dinophyta, Fungi, Metazoa, etc. The appearance of thecate dinoflagellates, thin-walled phytoplankton and "naked" unicellular organisms indicates that our method could obtain the intact DNA of organisms with different cell coverings. All the results demonstrate that our method is useful for DNA extraction of phytoplankton and environmental surveys of their diversity and abundance.

SUBMITTER: Yuan J

PROVIDER: S-EPMC4517865 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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An Improved DNA Extraction Method for Efficient and Quantitative Recovery of Phytoplankton Diversity in Natural Assemblages.

Yuan Jian J Li Meizhen M Lin Senjie S

PloS one 20150728 7

Marine phytoplankton are highly diverse with different species possessing different cell coverings, posing challenges for thoroughly breaking the cells in DNA extraction yet preserving DNA integrity. While quantitative molecular techniques have been increasingly used in phytoplankton research, an effective and simple method broadly applicable to different lineages and natural assemblages is still lacking. In this study, we developed a bead-beating protocol based on our previous experience and te ...[more]

PMID: 26218575

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Project description:BACKGROUND:Phenolic acids are a major group of secondary metabolites widely distributed in plants. In the case of maize, the major proportion of these metabolites occurs in the edible grain and their antioxidant activities are associated with improvements in human health. However, conventional extraction of secondary metabolites is very time consuming and generates a substantial amount of solvent waste. One approach to resolve these limitations is the use of microscale approaches, which minimize the quantity of solvents required, as well as the sample amounts and processing times. The objective of this work was to develop an improved microscale method for extraction of phenolic acids from maize and to compare it with a conventional extraction method. RESULTS:The improved microscale extraction method, coupled with an HPLC-DAD detection method, allowed identification of ferulic acid, p-coumaric acid in its free and bound form, and some diferulic acids. In its free form, p-coumaric acid ranged in content from 2.4 to 6.5 µg/g dry weight (dw) using the conventional method and 7.7 to 54.8 µg/g dw using the improved microscale method. Free ferulic acid content ranged from 2.6 to 12.9 µg/g dw for the conventional method and 16.8 to 181.7 µg/g dw for the improved microscale method. In its bound form, p-coumaric acid ranged in content from 6.0 to 30.6 µg/g dw for the traditional method and 34.4 to 138.6 µg/g dw for the improved microscale method. Bound ferulic acid ranged from 131.8 to 427.5 µg/g dw for the conventional method and 673.8 to 1702.7 µg/g dw for the improved microscale method. The coefficient of variation associated was lower for the improved microscale method than for the conventional method, thereby assuring the replicability of the process. CONCLUSIONS:The improved microscale method proposed here increases the extraction power and batch capacity, while reducing the sample quantity, solvent amounts and extraction time. It also achieves a better replicability with a lower coefficient of variation than is possible with conventional extraction.

Dataset Information

An Improved DNA Extraction Method for Efficient and Quantitative Recovery of Phytoplankton Diversity in Natural Assemblages.

Publications

An Improved DNA Extraction Method for Efficient and Quantitative Recovery of Phytoplankton Diversity in Natural Assemblages.

Similar Datasets

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