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Last Updated: Tuesday, 27 March 2007, 11:45 GMT 12:45 UK
Genome pioneer fishes for diversity
By Emilie Flaberg

On board Sorcerer II. Image: J Craig Venter Institute
It's clear that we have only begun to scratch the surface of understanding the microbial world around us
Craig Venter
Aboard a yacht called Sorcerer II, which doubles as a floating laboratory, scientists have been collecting lifeforms in an unprecedented genetic treasure hunt.

The two-year long scientific adventure has seen Sorcerer II sail the world's oceans in an effort to tap its riches.

The project aims to sequence genomes from the vast range of microbes living in the sea, to provide scientists with a better understanding of the evolution and function of genes and proteins and the environments to which they are adapted.

The man behind this ambitious project is scientist and entrepreneur Dr Craig Venter.

Ten years ago, Dr Venter came to global fame - and considerable fortune - through the race to sequence the human genome.

With his private venture Celera Genomics, he took on the major public sector laboratories with his excitingly named "shotgun sequencing" technique, catching the attention of the business-friendly US Congress, and making the covers of leading news magazines.

Hidden world

Craig Venter. Image: AP
Craig Venter: One of science's more colourful characters
What some saw as his disregard for scientific conventions such as open access to data brought Venter opprobrium in some circles, and rivals questioned how much data Celera actually generated.

Nevertheless, the financial rewards were enough to leave him in a highly unusual position for a scientist - with enough money and resources to do the science he wanted without having to tap the usual bureaucratic sources for funding and infrastructure.

Now, with his yacht-based lab, Dr Venter is embarking on an endeavour that is no less extraordinary in scope and imagination.

Revealed in a series of recent scientific papers in the journal Public Library of Science (PLoS) Biology, he says Sorcerer II is "...providing an unprecedented level of new genes and protein family discoveries" from the world's oceans.

"Given these findings, it's clear that we have only begun to scratch the surface of understanding the microbial world around us."

'New era'

The goal of the two-year Sorcerer II Global Ocean Sampling (GOS) Expedition was to shed light on the role of marine microbes by sequencing their DNA, without first needing to isolate individual organisms.

Sampling equipment. Image: J Craig Venter Institute
Water was systematically sampled every 360km along the route
Through random sampling of the genomes found in the environment, also known as metagenomics, the limitations of investigating only those microbes suited to growing in a laboratory are bypassed.

Most previous knowledge has come from only 1% of existing micro-organisms that can be maintained or cultivated in a lab.

"We know so little about the organisms in our environment, mostly because we have lacked the genomic and computational tools for understanding and examining these organisms," comments computational scientist Dr Doug Rusch, another of the research team.

"We believe that... the new tools we developed will help to unleash a new era of enhanced knowledge of the biological processes of microbial communities, and that this new understanding will begin to unlock the mysteries of unseen life."

Exceptional riches

During its recent 8,000km (5,000 miles) cruise which took in the North Atlantic, the Panama Canal, the Galapagos Islands and French Polynesia, the crew of Sorcerer II collected samples of surface water every 360km (200 miles).

At each sampling point, the water was directed through a series of fine filters, sorting particles such as microbes by size, so saving a mishmash of genetic fingerprints from the big blue.

The filters were immediately frozen on board in order to have the microbial material intact during its journey back to land.

Back at the J Craig Venter Institute laboratory in Rockville near Washington DC, the frozen filters were chopped up and the microbes stripped away by chemicals, leaving only the precious DNA to be analysed thoroughly.

The analysis was done by shotgun sequencing, where DNA is forced by high pressure through a tiny nozzle, breaking strands of genetic material into fragments.

THE DNA MOLECULE
DNA molecule, BBC
The double-stranded DNA molecule is held together by four chemical components called bases
Adenine (A) bonds with thymine (T); cytosine(C) bonds with guanine (G)
Groupings of these "letters" form the "code of life"; a code that is very nearly universal to all Earth's organisms
Written in the DNA are genes which cells use as starting templates to make proteins; these sophisticated molecules build and maintain an organism

Each fragment is sequenced, or analysed, to find the order of bases (the A, C, G and T molecules that "store" genetic information). Later, a computer can reassemble data from the fragments into an entire genomic strand, and individual genes can then be studied in detail.

Analysis of the microbial bounty revealed an exceptional data set of 7.7 million DNA sequences totalling 6.3 billion base-pairs.

It predicts that there should be more than 6.1 million proteins out there, nearly doubling the number we know of today, and shows that the world's oceans contain a huge diversity of naturally occurring microbial populations, both within and between sampling areas.

Many of the results surprised the scientists - the genes found in the cluster of new protein families showed a much higher number of sequences of viral origin than expected, pointing towards hitherto unrecognised diversity of viruses in the oceans.

One of Craig Venter's long-held visions has been to create genetically modified organisms designed to be "biofactories", making substances useful to humans in a world challenged by climate change and other environmental pressures.

The factories would produce hydrogen and ethanol for fuel, secrete non-polluting heating oil, and perhaps even absorb and process greenhouse gases.

It is too early to say whether Sorcerer II has found anything which can help drive this vision into reality; but the results do show that there is much more variety to the substances produced in nature than current textbooks would suggest.

Constituting half of the world's biomass and providing a fundamental ecosystem that recycles nutrients supporting life on Earth, marine microbes are an essential part of the planet's biodiversity.

Perhaps a fuller understanding of their origins, evolution and functions could illuminate their impact on our world, and reduce our impact on theirs.

Sorcerer II route map. Image: J Craig Venter Institute




SEE ALSO
Venter revives synthetic bug talk
04 Jul 05 |  Science/Nature
Scientists use DNA to make virus
13 Nov 03 |  Science/Nature
Gene pioneer's next goal
03 Oct 02 |  Science/Nature
Venter tackles global warming
30 May 02 |  Science/Nature
Genome pioneer steps down
22 Jan 02 |  Science/Nature
Code crackers to settle differences
18 Feb 01 |  San Francisco
The maverick: Craig Venter
30 May 00 |  Human genome

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