Three years after reporting the first pilot results from his Global Ocean Sampling (GOS), J. Craig Venter and colleagues have published a major new metagenomic survey of marine life.
J. Craig Venter’s GOS has sequenced 6.3 billion base pairs of DNA and identified 1.2 million new genes, according to three papers published this week in the open-access journal, PLoS Biology.
“Our results highlight the astounding diversity contained within microbial communities, as revealed through whole-genome shotgun sequencing carried out on a global scale,” Venter and co-authors, led by Douglas Rusch. “Our ability to make these observations derived from not only the large volumes of data but also from the development of new tools and techniques to filter and organize the information in manageable ways.”
The papers report the results of the 8,000 km journey of the Sorcerer II, Venter’s “floating lab,” that began sampling marine microbes from Nova Scotia to French Polynesia in February 2003. After the Sargasso pilot study (see “Venter Makes Waves Again,” Bio-IT World, April 2004), Venter sailed down the eastern coast of North America, the Caribbean, through the Panama Canal, and into the South Pacific. The team dropped anchor every 200 miles to collect ocean samples, including sampling in several locations around the Galapagos Islands.
The group studied 41 samples (including data from the pilot study) of marine planktonic microbiota collected from water at the ocean’s surface, about one foot deep in Ecuador, to more than 4,500 meters deep off of Mexico’s Yucatan Peninsula. The filtered samples were subject to genome shotgun sequencing and assembled using a modified version of the Celera Assembler program.
The results were astonishingly varied. Scientists made 7.7 million sequencing reads covering 6.3 billion base pairs of DNA. 85% of the data was assembled into sequences and 57% of the data that wasn’t assembled was unique according to a 98% cutoff. Researchers identified genes for a total of more than 6 million proteins covering nearly all prokaryotic protein families with some representing new families.
Within the abundant species found, the study showed many changes in genes across the data that suggest evolutionary adaptations, and genetically isolated populations that showed evidence for distinct environmental preference among the organisms.
For example, Rusch said, “some samples were similar to each other but geographically separated.” Some cyanobacteria found in the Caribbean and in the Pacific west of Central America were identical except for higher levels of phosphate binding proteins. “The Atlantic reads had the higher abundance of phosphate proteins,” recalls Rusch. “You can’t tell the populations apart from the Atlantic and Pacific except for the phosphate-binding proteins.”
The phosphate-binding proteins are an example of specific functional adaptations that could be seen across species and the population as a whole. Other populations showed adaptations for proteorhodopsin spectral tuning using light to trigger a H+ pump.
For the full text, please see:
Email Allison Proffitt.
Subscribe to Bio-IT World magazine.