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

Robert K. Naviaux; Benjamin Good; John D. McPherson; David L. Steffen; David Markusic; Barbara Ransom; Jacques Corbeil

doi:10.3354/meps301009

MEPS

Marine Ecology Progress Series

via Mailchimp

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

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

Robert K. Naviaux^1,*, Benjamin Good^2,6, John D. McPherson³, David L. Steffen³, David Markusic^1,7, Barbara Ransom^4,8, Jacques Corbeil^2,5

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

*Email: naviaux@ucsd.edu

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

Full text in pdf format

Export citation
Share: Facebook - - linkedIn

Cited by

Previous article Next article

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

Robert K. Naviaux^1,*, Benjamin Good^2,6, John D. McPherson³, David L. Steffen³, David Markusic^1,7, Barbara Ransom^4,8, Jacques Corbeil^2,5