MEPS 301:9-22 (2005)  -  doi:10.3354/meps301009

Sand DNA—a genetic library of life at the water’s edge

Robert K. Naviaux1,*, Benjamin Good2,6, John D. McPherson3, David L. Steffen3, David Markusic1,7, Barbara Ransom4,8, Jacques Corbeil2,5

1The Mitochondrial and Metabolic Disease Center, Departments of Medicine and Pediatrics, Room C-103, Building CTF, San Diego School of Medicine, University of California, 214 Dickinson Street, San Diego, California 92103-8467, USA
2Genomics Core Laboratory, Center for AIDS Research and Veterans Medical Research Foundation, Room 325, Stein Clinical Research Building, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0679, USA
3Department of Molecular and Human Genetics, and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, N1519, Houston, Texas 77030, USA
4The Scripps Institute of Oceanography, Geosciences Research Division, La Jolla, California, USA
5Laval University, Québec, Canada
6Present address: Department of Molecular Biology and Biochemistry, Room SSB 8166, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
7Present address: Meibergdreef 69-71, Amsterdam 1105 BK, The Netherlands
8Present address: The National Science Foundation, Geosciences Office, 4201 Wilson Boulevard, Arlington, Virginia 20036, USA

ABSTRACT: Powdered silica has long been used for the purification of nucleic acids in the laboratory. Silicate-rich, ordinary ocean beach sand was found to concentrate dissolved DNA from seawater over 10000-fold, providing a rich, renewable, and easily accessible genetic library that is easy to harvest and inexpensive to process. We found an average of 29 µg ml–1 of cell-free DNA adsorbed to silicate-rich, wave-washed sand from 14 beaches bordering 9 seas around the world. The DNA from a reference beach was shotgun cloned, 3107399 nucleotides of anonymous, non-redundant sequence were analyzed, and 2571 genes were found; 2562 of these genes were new. The apparent complexity of sand DNA was greater than 1.4 × 1011 nucleotides. About 90% of the sequences identified were from prokaryotes, 10% from eukaryotes, and 1% were viral. Sequences from all kingdoms of life were present. Over half the sequences came from new phylotypes, reflecting the novelty of this genetic reservoir.


KEY WORDS: Sand · Genetic library · Dissolved DNA · Beach


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