Abstract
When collecting sediment samples, caution is needed to prevent contamination from outside microorganisms and altered quality of the sediment during deposition. Extraction from marine sediments involves the disruption of the microbial cells to dissolve the genomic DNA into extraction buffer and the purification of the DNA from the extraction buffer. Bacterial disruption can be achieved using cycles of freezing and thawing, pulverizing cells using beads, and degrading the cell membrane using detergents and/or enzymes, such as protease and/or lysozyme. DNA are purified from the extraction buffer by organic solvent extraction and/or adsorption to silica materials. Marine sediments often contain large amounts of humic substances. Polysaccharides are also contaminated in the DNA extract sometimes. These materials inhibit PCR, so removal treatments are required. DNA yield, extraction efficiency, and grade of purification differ in each method and depending to sediment sample qualities. Various commercial kits for DNA extraction from environmental samples are available. A method appropriate to the purpose of the study should be selected.
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Sakami, T. (2019). Collection of Microbial DNA from Marine Sediments. In: Gojobori, T., Wada, T., Kobayashi, T., Mineta, K. (eds) Marine Metagenomics. Springer, Singapore. https://doi.org/10.1007/978-981-13-8134-8_2
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DOI: https://doi.org/10.1007/978-981-13-8134-8_2
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