Sequence and Consequence – Genomic Exploration of the Sargasso Sea

The Sargasso Sea, named after the type of floating algae called Sargassum that riddles its surface, is a two million- square-mile ellipse of deep-blue water that lies in the North Atlantic. This sea’s position drifts only slightly as a result of seasonal temperature fluctuations despite being surrounded by some of the strongest currents in the world: The Florida, Gulf Stream, Canary, North Equatorial, Antilles, and Caribbean currents. These interlock to separate the Sargasso Sea from the rest of the tempestuous Atlantic, which results in a slow, clockwise rotation of the waters within. The algae that reside at the surface of the Sargasso Sea provide a deceptively lush veneer to a body of exceptionally warm and clear water traditionally described as being devoid of life at deeper levels. But even in this ocean ‘desert’ there is an intricate web of life that has adapted to existence among the Sargassum.

In 2003, controversial genomics entrepreneur Craig Venter, famed for commercializing the human genome sequence, obtained guaranteed funding of USD 9 million over three years to sequence the DNA of every microscopic organism within the waters of the Sargasso Sea (1).

Venter stepped down as president of Celera in early 2002 in order to head up the Institute for Biological Energy Alternatives (IBEA), which is involved in the Sargasso Sea project. Many claimed that this move was symptomatic of the inevitable industry-wide shift in focus from gathering genome information to the development of new drugs, but Dr. Venter is hoping to put a vast body of unexplored genomic information to work in developing novel energy production technologies.

At first glance it may seem out of place that funding for this project be provided by the US Department of Energy (DOE), but this should come as no surprise considering the expansion of projects funded by the DOE into the realm of biological research. Specifically, the DOE has established a biomass program which, it explains, ‘…develops technology for conversion of biomass (plant-derived material) to valuable fuels, chemicals, materials and power, so as to reduce dependence on foreign oil and foster growth of biorefineries’ (2). The DOE further states that ‘Biomass is one of our most important energy resources. The largest US renewable energy source every year since 2000, it also provides the only renewable alternative for liquid transportation fuel.’ – a formidable admission considering that non renewable energy sources currently drive the US economy (3).

It is widely recognized that the development of energy producing technologies that utilize biomass would strengthen rural economies, decrease America’s dependence on imported oil, avoid use of highly toxic fuel additives, reduce air and water pollution, and reduce greenhouse gas emissions. Current biomass uses include ethanol and biodiesel production, along with biomass power and industrial process energy. In the future, it is entirely plausible that bioreactors will employ advanced technologies, involving biological catalysis, in the production of both biopolymers and fuels. In effect, there would be considerable benefits to developing these technologies, and this is where Dr. Venter and the IBEA come in.

Dr. Venter wants to contribute important new knowledge for finding solutions to energy problems. He has stated that “With fossil fuel consumption continuing to rise and with its serious environmental damage to our planet, it is imperative that we explore alternative ideas to abate this situation” (4), and he clearly has the backing of the US DOE in exploring these alternatives.

At a lecture given at the Conference for the International Society for Microbial Ecology (ISME) in August 2004, Dr. Venter placed a heavy emphasis on environmental issues. Specifically, he stated that ‘the Environment is more important than any issue within the biological realm today’, and in saying so revealed his true colours as an environmentalist. He could easily be basking in the success of his achievements, but is rather working towards finding solutions to the impending world energy crisis which looms menacingly on the nearing horizon.

He expressed disgust at the state in which his team has found the oceans that his team has sampled. He has warned that they cannot work under the assumption that the oceans are in a pristine state, as evidenced by the fact that his group has, on many occasions, found human fecal bacteria in waters heavily trafficked by cruise ships which dump their raw sewage directly into the ocean. He went further to explain that ‘you cannot go a mile in the ocean without finding floating plastic and other debris. In fact, on one occasion we came across a floating refrigerator which the crew was eager to search for beer’.

In April of 2004, Dr. Venter and his colleagues announced the preliminary results of their project (5). They sampled and catalogued microbes in the Sargasso Sea, and used the “whole genome shotgun sequencing approach” (at the heart of which lies an algorithm capable of reassembling the genomic sequences that are broken apart by the technique) to map the DNA of thousands of microbes from the ocean simultaneously, making their results available through a public database (6).

Their results identified 1800 species of microbes, including 150 new species of bacteria, and over 1.2 million new genes, and although the function of the majority of these genes is unknown, the research is a first step to understanding more about life in the Sargasso Sea and the larger ocean.

The number of genes identified in these samples from the Sargasso Sea is striking and suggests that the microbial life in the ocean is far more abundant and diverse than previously expected. This is especially interesting considering that the Sargasso Sea was initially chosen because it was thought to contain a relatively small number of species owing to its low nutrient levels.

In his ISME lecture, Dr. Venter stated that the single most interesting finding was the abundance of photorhodopsin-like genes in the Sargasso Sea. The presence of these photorhodopsins could account for the number of species isolated from the Sargasso Sea in that photobiology is likely a key source of energy in this relatively nutrient poor environment.

Dr. Venter’s project has now evolved into an expedition that will provide insights into the microbial diversity in all the oceans of the world. Once completed, his voyage will have taken samples from some 3000 sites ranging from Halifax, Nova Scotia, to the Galapagos Islands in the Pacific Ocean. The planned course of this expedition follows in the wake of the HMS Challenger, which sailed around the world in the 1870’s with the aim of resolving whether there was life to be found deeper than 200 metres below the surface of the ocean, a highly controversial question at the time.

What Venter and researchers at the IBEA hope to find are unique genes or microbes that could create alternative sources of energy or clean up the environment.

In their own words ‘the IBEA was founded with the goal of exploring biological mechanisms for dealing with carbon sequestration and to study the creation of other potential energy sources such as hydrogen. We believe that building a synthetic chromosome is an important step toward realizing these goals because we could potentially engineer an organism with the ideal qualities to begin to cope with our energy issues.’, and he says that the oceans are the perfect spot on earth to start looking for potential solutions.

In theory, a novel gene could, for example, help scientists engineer microbes to make clean fuels such as hydrogen or to clean up toxic wastes.

Interestingly, preliminary results from the Sargasso Sea project identified over 700 novel genes that are thought to play a role in helping bacteria capture energy from the sun. This is hundreds more than have been found before, and studying them would bring researchers closer to the possibility of the microbial production of hydrogen.

Technologies involving the microbiological breakdown of toxic compounds such as perchlorate (an additive to solid rocket fuel), chlorinated benzene chemicals (components of paints and industrial solvents), heavy metals, and organophosphates (a family of neurotoxins commonly used as pesticides) have already been described. Expanding the list of known genes will only act to increase the number of functionalities that can be used to engineer microbes for specific applications.

In conjunction with the Sargasso Sea project, Dr. Venter has been focusing on the study of Mycoplasma genitalium, a bacteria with the smallest known genome, with the intention of engineering a minimal living cell and adding useful functionalities to it.

The ability to create a living cell from scratch is beyond present technology, but Dr. Clyde Hutchinson demonstrated an alternative solution in 1999 by trying to define the minimum number of genes that Mycoplasma genitalium required for survival by removing all of the nonessential ones.

Hutchinson reported that Mycoplasma genitalium could survive with as few as 265 genes, and that this set could be thought of as the minimal complement of genes needed to sustain life. Dr. Venter has resumed Dr. Hutchison’s project, and hopes to first succeed in creating a minimalist organism and to then add specific functions to it for use in applications such as hydrogen production or waste degradation. In essence, not only is he working on identifying useful genes, but he is working towards creating a host for those genes that can be manipulated.

The data gathered on the Sargasso Sea expedition is only a starting point. The analysis and interpretation will continue for years, and will provide the basis for future experiments. Both Dr. Venter and his colleagues admit that they are still ‘a long way from understanding the biology of these organisms… [because] without physical and basic microbiology, genomics cannot answer all the questions we need to know in terms of the microbes that make up the ocean.’.

However, their research is an important first step in the search for the molecular tools upon which future technologies will be based.

Dr. Venter’s closing remark at the ISME conference was simple and to the point. He stated that ‘As the Sorcerer II sails on, we hope to leave a lot of new data in our wake’, and it is becoming evident that this is the case.

References

1. Article available online through the United States Department of energy site: http://www.energy.gov/engine/content.do?PUBLIC_ID=14450&BT_CODE=DOEHOME&TT_CODE=PRESSREL EASE

2. Article available online through the United States Department of energy site: http://www.energy.gov/engine/content.do?PUBLIC_ID=13051&BT_CODE=PR_PRESSRELEASES&TT_CODE= PRESSRELEASE

3. Article available online through the United States Department of Energy, Energy Efficiency and Renewable Energy site: http://www.eere.energy.gov/biomass/

4. Article available through the National Post online: http://www.gairdner.org/news52.html

5. J.C. Venter et al., Science 304:66 (2004).

6. Data is available through the Whole Genome Sequencing page at Genbank: http://www.ncbi.nlm.nih.gov/Genbank/WGSprojectlist.html

7. The project accession number AACY01000000 (environmental sequence)

The Sorcerer II expedition can be followed at: http:/www.sorcerer2expedition.org/main.htm

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