Book Review: “The Voyage of Sorcerer II” — Sampling Microbes in the World’s Oceans

By Pat Reber

If you want to see how Earth’s oceans are coping with global warming, what better way than to sail around the world for 15 years — and have a little fun doing it?

The Voyage of Sorcerer II: The Expedition that Unlocked the Secret of the Ocean’s Microbiome, by J. Craig Venter and David Ewing Duncan. The Belknap Press of Harvard University Press,  302 pages, $27.95.

J. Craig Venter, the biochemist and geneticist who led one of the first draft sequences of the human genome in 2000, turned his yacht Sorcerer II into a floating research vessel three years later. He and his crew set out to assess genetic diversity within marine microbial communities: the life of bacteria, viruses, proteins, phytoplankton, and other tiny species in Earth’s waters that maintain the planet’s health.

Phytoplankton and other microbes produce at least half of the planet’s oxygen. They absorb through photosynthesis approximately 25 to 30 percent of the atmosphere’s carbon dioxide. Venter’s goal was to establish the first global database for the microbiome. The importance of his quest will be clear to anyone interested in the vital role oceans play for all life on our planet.

When Venter announced his project, eyeballs rolled over his comparison of his voyage with the 19th-century travels of one of the world’s most famous scientists, Charles Darwin, on the HMS Beagle.

But his claims as an adventurous pioneer hold up under scrutiny. Venter’s personal journey started as a Navy corpsman in the Vietnam War. His experience there inspired him to later sequence the genome of every disease microbe — malaria, tuberculosis, cholera, hepatitis, meningitis — he had encountered in US soldiers fighting in Vietnam. He also helped sequence the Meningitis B bacterium, which contributed to the development of the first Meningitis B vaccine.

In The Voyage of Sorcerer II,  Venter is “thinking big about small.” During the team’s travels around the globe, they capture microbes by running 200 liters of seawater through a series of delicately refined filters at every stop, freezing them, and sending them back to the J. Craig Venter Institute in LaJolla, California, for “shotgun sequencing.”

Shotgun metagenomic sequencing involves chopping up complex source material — in this case, the microbial matter on the filters — into little pieces and using computers to identify overlapping strands of DNA to reassemble individual genomes. The shotgun processing of such complex material began with the analysis of the microbes found in the Sargasso Sea during Sorcerer II’s 2003-2006 circumnavigation. That has become credited as one of the key drivers for what has become modern metagenomics.

Most people know that the ice caps are melting and oceans are becoming warmer. In July alone, temperatures rose above 100 degrees F in the waters off Florida. Venter wanted to see the effect on the phytoplankton living near the surface, where the normal flow of nutrients from deeper in the water — the so-called ocean carbon biological pump — may be interrupted because of the increasing temperatures. This development could starve out some varieties of the phytoplankton, thus reducing the absorption of the carbon dioxide responsible for global warming.

The expedition journeyed through all of Earth’s major oceans and seas and took samples above the Arctic Circle and in Antarctica, where they found plankton clinging to the underside of the ice, protected from Antarctic krill, which like to eat it. Venter and crew dipped into the outflow of river deltas to probe the effect of human pollution on the waters.

What Venter found in his mission reinforces his belief in the “urgency” to catalogue what’s there now and “how it was changing, to establish a baseline of fundamental scientific knowledge.” His conclusion regarding our complacency in the resilience of nature is alarming: “Most of us have such a human-centric view of the world, like the Earth was made for us and it will keep supporting us no matter what we throw at the environment. Even some biologists tend to focus on the environment that supports humans like it’s set in stone, or it’s the gold standard of what life is, which is kind of disastrously wrong.”

Venter is also a businessman with degrees in biochemistry and pharmacology, who has made no secret of his hopes that the expeditions on Sorcerer II will identify microbes that could provide alternative energy sources or medical benefits.  He is the founder, chairman, and CEO of the J. Craig Venter Institute, a nonprofit research organization. He is cofounder of the biotechnology companies Celera, Synthetic Genomics, and Human Longevity. In May 2010, Synthetic Genomics — in the midst of Venter’s ocean expeditions — raised ethical concerns with the announcement that his team was the first to successfully create “synthetic life” by producing a single-cell bacterium. The possibility that Venter’s expeditions could find financially exploitable microbes brought charges of “biopiracy” from at least one environmental group. Some of the countries in whose waters he fished required permits to do the sampling.

For instance, Venter’s venture into the Sargasso Sea — long declared to be a biological desert — was alarming for Bermuda. The excursion produced a surprising picture of microbiome diversity, including 148 never-before-seen species of bacteria, which confounded his naysayers. “Here we discovered over a million genes in Bermuda’s water,” Venter writes, “and the implication in Bermuda was that we patented (emphasis author’s) a million genes. But the team did not patent anything. Everything went into the public domain.”

Brazil insisted that the microbial material found in its waters be analyzed in its own laboratories. Ecuador raised concerns about research around the Galapagos Islands. More than 15 countries requested permits for Venter’s sampling, a list that included Mexico, Panama, Britain, Germany, and Sweden.

Much of The Voyage of Sorcerer II focuses on detailed scientific matters rather than political/economic issues. There are references to the many journal articles the expeditions have already produced. Another challenge for the nonscientist: the involvement in the book of Venter’s co-author, David Ewing Duncan, a science writer. At times it is difficult to determine whose voice is speaking.

Still, Duncan also makes Sorcerer II’s logs come alive. We sense there is adventure afoot. While team members are exploring Antarctic ice, they are surprised by Weddell seals popping up to breathe through the research holes. Emperor penguins gather to watch them work. In Sweden, Venter invites King Carl XVI Gustaf on board for drinks and the scientist joins one of the boats competing in the Volvo Ocean Race (formerly Whitbread Around the World race) that is taking place as Sorcerer II arrives in Stockholm.

At the beginning of one of its voyages the crew stops for slices of blueberry pie in the Bay of Fundy. Jeff Hoffman, a scientist on board for most of the expeditions, jumps into the water in 2010 to join the Byron Hellespont Bicentenary Swim in Çanakkale, Turkey.

From 2003 to 2018, Sorcerer II covered 65,000 nautical miles as it explored the Pacific, Indian, and Atlantic Oceans, and the Baltic, Mediterranean, Aegean, and Black Seas. Over that period the vessel encountered strong winds and rough seas. It needed periodic months-long maintenance work in dock.

The team extracted a total of 477 samples, including 147 taken during the 2003-2006 circumnavigation, and another 218 samples taken on land, such as those procured in the Arctic and Antarctic. Here is just one concrete result: the team’s sampling in the Antarctic produced a first-time analysis of the green sulfur bacteria Chlorobiaceae, which plays an important role in how carbon and sulfur cycle globally. The team’s first scientific paper, released in 2007 as the Ocean Metagenomics Collection, focused on the first 41 samples taken from Halifax to the Galapagos, including the Sargasso Sea. The analysis produced 7.7 million genetic sequences containing 6.3 billion base pairs, plus 6.12 million proteins and 154,662 viral peptide sequences and viral scaffolds.

Millions of microbes remain frozen in the La Jolla labs waiting to be sequenced and analyzed over years to come — a “treasure trove of Earth’s smallest life.”

Pat Reber, 76, a retired journalist living in Maryland, has worked as a reporter and editor in New York, Washington, DC, Germany, Kenya, and South Africa. While serving as deputy bureau chief in Washington for Deutsche Presse-Agentur (dpa) during the Bush and Obama years, her reporting beat was climate change. She covered the UN climate talks in Durban (2011) and Paris (2015). She last wrote a review for ArtsFuse on Writing for their Lives: America’s Pioneering Female Science Journalists by Marcel Chotkowski LaFollette.

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