Year: 2007
Type: article
Abstract: Being invisible to the naked eye, microbes managed to escape scientific scrutiny until the mid-17th century, when Leeuwenhoek invented the microscope. These cryptic organisms continued to thwart scientists' efforts to probe, describe, and classify them until about 40 years ago, owing largely to a limited morphology that defies traditional taxonomic methods and an enigmatic physiology that makes them notoriously difficult to cultivate.
Most of what we know about the biochemical diversity of microbes comes from the tiny fraction that submit to lab investigations. Not until scientists determined that they could use molecular sequences to identify species and determine their evolutionary heritage, or phylogeny, did it begin to become apparent just how diverse microbes are. We now know that microbes are the most widely distributed organisms on earth, having adapted to environments as diverse as boiling sulfur pits and the human gut. Accounting for half of the world's biomass, microbes provide essential ecosystem services by cycling the mineral nutrients that support life on earth. And marine microbes remove so much carbon dioxide from the atmosphere that some scientists see them as a potential solution to global warming.
Yet even as scientists describe seemingly endless variations on the cosmopolitan microbial lifestyle, the concept of a bacterial species remains elusive. Some bacterial species (such as anthrax) appear to have little genetic variation while in others (such as Escherichia coli) individuals can have completely different sets of genes, challenging scientists to explain the observed diversity.
The emerging field of environmental genomics (or metagenomics) aims to capture the full measure of microbial diversity by trading the lens of the microscope (and biochemistry) for the lens of genomics (and bioinformatics). By recovering communities of microbial genes where they live, environmental genomics avoids the need to culture uncooperative organisms. And by linking these data to details relating to sequence collection sites, such as pH, salinity, and water temperature, it sheds light on the biological processes encoded in the genes.
The largest metagenomic dataset collected so far comes from the Sorcerer II expedition, named after the yacht J. Craig Venter transformed into a marine research vessel. In a pilot study of the Sargasso Sea, Venter's team identified 1.2 million genes and inferred the presence of at least 1,800 bacterial species. But the genetic and taxonomic diversity of the data imposed new challenges on existing genome assembly methods and other analysis techniques. The researchers designed the Sorcerer II Global Ocean Sampling (GOS) expedition to see if collecting more samples would improve their assembly and lead to a better estimate of the number and diversity of microbial genes in the oceans.
And now, in three new studies, Venter's team has combined the expedition's latest bounty—6.5 million sequencing “reads”—with the Sargasso Sea data. The result is a geographically diverse environmental genomic dataset of 6.3 billion base pairs—twice the size of the human genome. (To learn about the voyage and sampling methods, see Box 1.) In the first paper, Douglas Rusch, Aaron Halpern, and colleagues attempt to describe the immense amount of microbial diversity in the seas, and determine how—or if—that diversity is structured and what might be shaping that structure. In the second paper, Shibu Yooseph et al. study the millions of proteins in the GOS sequences to see if we're close to discovering all the proteins in nature. And in the third study, Natarajan Kannan, Gerard Manning, and colleagues classify thousands of kinases into 20 distinct families, revealing their structural and functional diversity and an unexpected importance in prokaryotic regulation.
Box 1. Following the Sorcerer II's Hunt for Microbes
The Sorcerer II expedition was inspired by the British Challenger expedition (1872–1876), a pioneering oceanography research project that discovered hundreds of new genera and nearly 5,000 new marine species. Its gun stations replaced with research stations, the Challenger circumnavigated the oceans, stopping every 320 kilometers to recover specimens from bottom, intermediate, and surface depths to explore the diversity of macroscopic marine life. At each stop, the crew recorded the location, what they used to extract the sample, the depth of the sample, and several observations related to water and atmospheric conditions. The Sorcerer II followed a similar sampling schedule, traveling nearly 9,000 kilometers to collect samples of microbial marine life and record the water's location, depth, pH, salinity, and temperature.
H.M.S. Challenger (Image: NOAA, Steve Nicklas)
The GOS crew collected samples from surface waters of diverse, mostly marine aquatic environments. The samples were collected between August 2003 and May 2004 during a six-leg journey that followed a path from northeastern Canada to the South Pacific Gyre. Venter's crew collected microbial samples by pumping 200 liters of surface seawater through a series of increasingly fine filters, which they labeled, froze, and sent back to the lab of the J. Craig Venter Institute in Maryland.
After a stop in the Gulf of Maine, the expedition sampled three sites along Nova Scotia, including a “highly eutrophic” coastal embayment in Halifax. The crew set sail again in November, starting in Newport Harbor, Rhode Island, and ending in the Delaware Bay, one of several estuaries targeted on the journey.
The next leg began in Chesapeake Bay. The largest US estuary, Chesapeake Bay contains a rich mix of freshwater and marine organisms. Estuaries are complex hydrodynamic environments that are highly sensitive to runoff from agricultural and urban development (which can dump massive amounts of nitrogen and phosphorous into watersheds). Microbial communities collected from estuaries promise to provide valuable insights into the metabolic and physiological adaptations required by such environments. Continuing down the Atlantic seaboard, the expedition stopped near Cape Hatteras, North Carolina, and the Florida Keys before passing through the Caribbean and ending near Panama, where the crew collaborated with scientists at the Smithsonian Tropical Research Institute.
The fourth leg of the voyage sampled sites in the Eastern Pacific, including Cocos Island, about 500 kilometers southwest of Costa Rica. A highly productive ecosystem inhabits the waters off the island, a result of ocean currents buffeting the coast and causing nutrient upwellings that mix with warm surface waters. The crew made one last stop in the open ocean, then headed for the Galapagos Islands.
Owing in part to its position near major ocean currents and atmospheric transition zones, the Galapagos Archipelago sits within a hydrographically complex region. Unique oceanographic features there support a diverse set of habitats and endemic species, found within several discrete zones distinguished by temperature. This microbial mother lode held the crew's attention for two months, while they extensively sampled the region.
By early March 2004, the crew had collected the last three samples used in these studies, from two open ocean sites and a lagoon in a coral reef in the South Pacific Gyre. Follow these links to learn more about the Sorcerer II (http://www.sorcerer2expedition.org/version1/HTML/main.htm) and the Challenger (http://hercules.kgs.ku.edu/hexacoral/expedition/challenger_1872-1876/challenger.html) expeditions.
The Sorcerer II (Image: J. Craig Venter Institute)
Source: PLoS Biology
Author: Liza Gross
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $5,500
OpenAlex ID: W2139347221