Difficulties in efficient DNA extraction from deep-sea volcanic basalt, due to high metal concentration, complex organic matter, or sometimes the low biomass, have hampered the understanding of the significant biosphere both at and below the sea floor. In order to optimize the DNA extraction
from basaltic rocks, sterilized basalts with different particle sizes and chemically synthesized goethite were inoculated with an iron oxidizer Marinobacter aquaeolei and an extreme halophilic archaeon Halobaculum gomorrense respectively, and extracted with several methods. Large variations
in DNA yields by different extracting methods including FastDNA® spin for soil kit, GeneClean® for ancient DNA kit, UltraClean™ and traditional phenol-chloroform methods. Among the commercially available kits tested here, FAST spin kit and GeneClean® for ancient DNA kit yield
10 times more DNA than the UltraClean™ kit used. In combination with FAST spin kit, skim milk greatly enhanced the archaeal DNA yields. DNA extracting efficiency was low with the cell number lower than 1 × 106 cells, but reached as high as 88% with a cell number of 1 × 108
cells. On these points, different strategies should be taken into consideration for the DNA extraction from basalts, depending on original biomass and cell types anticipated. FAST spin kit could provide high quality bacterial DNA for downstream PCR whilst the combination of FAST spin kit with
skim milk would greatly enhance the archaeal DNA yields. GeneClean® for ancient DNA kit is also recommended for archaeal DNA extraction from deep sea basalt due to its high yield.
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Document Type: Research Article
Key Laboratory of Biogeology and Environmental Geology of Ministry of Education, China University of Geosciences, Wuhan, P. R. China,Geomicrobiology Group, Department of Biological Sciences, University of Southern California, Los Angeles, CA,
Geomicrobiology Group, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA,Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
Publication date: 2009-10-01
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