The Jeffs work on
Thursday 24th January
While some on the ship have got what John in the galley called ‘the channels’ and slipped into a kind of lethargy and listlessness associated with nearing home, the oceanography lab is pumping.
Some background first:
Three quarters of the Earth’s surface is water but it’s this vast frontier of ocean that we are only just starting to discover. The future, it seems, is microbiology.
As recently as 2004 a report in Science astounded the scientific community. It described the microbial diversity in water samples taken in the Sargasso Sea by the Venter Institute. This sea was selected specifically because of its low nutrient levels but remarkably, of the 1.045 billion base pairs sequenced from the water samples, 1.2 million previously unknown genes were discovered. The study showed between 10 and 100 times more microbial diversity of the ocean waters than previously reported and triggered the next phase of research.
In 2003 Craig Venter set up the Sorcerer 2 Global Ocean Sampling expedition. He converted a luxury yacht into a research vessel and mapped out a project over two years circumnavigating the globe, traveling 20,000 nm and visiting 16 countries, 7 territories and 57 different islands. Water samples were collected from the ocean every 200 miles as well as from targeted unique marine environments such as the Galapagos.
Jeff Hoffman was expedition scientist on Sorcerer 2 and he’s now on Voyage 3 with colleague from the Venter Institute, environmental genomics scientist, Jeff McQuaid.
A special CTD cast for the Jeffs is keeping them busy until we sight land. On V3 they are sampling surface water as we go but they have also taken deepwater samples down to 3000 metres for genomic analysis of marine micro-organisms near the seabed and some mid column samples where phytoplankton were present.
It’s a time-consuming business in the noisy oceanography lab. Each sample takes 6 hours to process. The water is pumped through a pre-filter that removes zooplankton, then it goes through a series of three very fine filters that capture diatoms and larger plankton, then pico-plankton and finally the bacteria and marine virus. Marine bacteria are thought to comprise the bulk of living organisms in the ocean, but they are the least studied due to their small size and the extreme difficulties in culturing them back in a laboratory. At the end the Jeffs have a small vial of viral concentrate and three filters which have captured the tiny forms of life.
The filters are preserved in a fixative, stored in sealed plastic bags and frozen at minus 80 degrees Celsius. They will be dispatched to the Venter Institute and collaborating institutions and universities around the world.
The laboratories will sequence the DNA and identify organisms based in the genetic material contained on the filters. It’s information that may hold many clues to the problems we face globally. There are organisms that can fix carbon, others thrive breaking down toxins, some micro-organisms adapt readily to changes in environment. There are applications for medicine, the environment and climate change.
For example, in the Sargasso Sea study, 11 novel hydrogenases were discovered. Hydrogenases are enzymes which can split water into hydrogen and oxygen, and have the potential to produce cheap and clean hydrogen as a fuel source.
Jeff told me he saw the light a few years ago. After studying the big animals he made the switch to microbiology. He explained that the oxygen environment we live in was created by photosynthetic bacteria, and it’s bacteria that controls the earth’s climate.
I’ve got a lot more time for bacteria now.
Pics: Jeff McQuaid at the filters, Jeff Hoffman in lab, Jeff collecting samples near iceberg (pic Esmee Van wijk)
Margot Foster is a journalist currently on board the Australian Aurora Australis, an Australian research vessel currently participating in the Census of Antarctic Marine Life (CAML, IPY project 53). She works with the Australian Broadcasting Corporation (ABC).