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Surveying the World's Marine Life

Eric Karsenti Talks About the Tara Oceans Expedition

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Surveying the World's Marine Life

Picture of Dr. Eric Karsenti

EMBO

Dr. Eric Karsenti, group leader at the European Molecular Biology Laboratories (EMBL) in Heidelberg gave a special presentation, A Forgotten World: The Living Ocean, at the 2012 European Molecular Biology Organization (EMBO) meeting.

A New Voyage of the Beagle

Dr. Karsenti, a renowned cell biologist, refocused his research to a more global perspective a few years ago. While reading Darwin’s account of his journey around the world in The Voyage of the Beagle, Dr. Karsenti mentioned that he was inspired to revisit that spirit of discovery in the 21st century. Of course, the trip recounted in the memoir is what precipitated Darwin's understanding of the natural world that eventually crystallized into the theory of evolution. Channeling his inspiration, exceptional energy, and profound intelligence, Dr. Karsenti soon coalesced the idea for a modern day oceanic scientific exploration into the Tara Oceans Expedition, a 62,000 mile 2.5 year global trip involving over 250 people from 35 different nations.

Cataloging All Ocean Life

The goal the Tara Oceans Expedition was both simple and dauntingly ambitious: to assess the worldwide diversity of ocean life. While most of us typically think of ocean life as the fish and other large sea life, in fact, it is one-celled organisms and other microscopic life that make up a whopping 98% of the ocean’s biomass. It is an astoundingly diverse and rich ecosystem that we know little about. It is this population that the Tara Expedition set out to catalog and initial results from the expedition suggest we know even less about it than we realized.

The Oceans Are the Key to Life on the Planet

Dr. Karsenti started out his presentation noting that virtually all the major developmental milestones leading to our living blue planet occurred in the oceans. The first life started approximately 4 billion years ago in the oceans. About 3.5 billion years later, symbiosis between these simple organisms developed into more complex eukaryotic cells, forming the first protists. It was these one-celled protists— in particular the diatoms—that changed the world and allowed for the appearance of multicellular life about 700 million years ago. The metabolism of these photosynthetic plankton oxygenated the Earth's atmosphere.

The Most Numerous Organisms in the World

Not familiar with diatoms? These plankton produce about 40% of the oceans biomass and over 20% of the oxygen in the atmosphere. Diatomaceous earth used in filtering and gardens is largely composed of these organisms, as are the limestone White Cliffs of Dover and the sandstone rocks used to make the Egyptian pyramids. Their oxygen-carbon exchange is more significant than all the trees in the Amazon but, as with much of microscopic ocean life, our knowledge of their biology, diversity, and ecology is quite limited. The Tara Expedition formed to address this huge blind spot in our understanding.

Sampling the Ocean's Diversity

The expedition adopted a cross-discipline integrative approach for both collections and analysis. Based on well documented stable ocean currents, as can be seen in this awe-inspiring dynamic animation of worldwide ocean currents put together by NASA, sampling sites with diverse environmental conditions (e.g., temperature, water sources, stable currents, etc) were selected at 153 locations around the globe.

At each sample location, various filters were cast in the sea to collect differently sized organisms, from one with a 20 micron cutoff to catch viruses, up to a 600 micron cutoff filter to catch the larger protists and one-celled colonies. Samples were taken at different depths.

Over 27,000 samples were collected in a two-year period worldwide. With each sample, various physical and chemical properties of the water, such as temperature, acidity, oxygen levels, etc. were acquired which will enable correlation of the organisms with their environmental parameters.

Other groups have conducted more regional surveys, such as Northeast Fisheries Science Center plankton surveys in the Atlantic. Also, there have been more globally focused projects to survey primarily bacteria, such as the J. Craig Venter Institute's expeditions. However, by sorting and collecting multiple types of microbes on filters sorted by size, at different depths, at locations defined by ocean currents, and correlating the samples with water chemistry, the Tara Expeditions, so far, is the most ambitious marine microbe survey completed.

Analyzing the Samples

Analysis of the samples involves two approaches: imaging and genomic DNA sequencing. Microscopic analysis of the various size filters yield visual images of the diverse array of organisms. Some of imaging was done right on-board at the collection sites. Back on land, other research labs connected with the project are working out high-throughput automated system with image recognition, the morphology of the organisms can be cataloged and sorted for each of the collection samples.

Despite the high-tech microscopy, systematic analysis of organisms morphological characteristics has a long history in the life sciences. After all, it was really this sort of data that provided the original basis for Darwin's theory of evolution. However, Darwin likely had no concept of the other 21st century technique that will be used to analyze the samples—genomic analysis. DNA sequencing is now hundreds of times faster than in the late 1990s when full human genome was being sequenced. It has reached a point that researchers can read tens of millions of DNA bases a day, and computers can routinely assemble highly diverse pools of short overlapping DNA fragments into a full genome (all of an organism DNA assembled together) containing 100 of billions of bases.

However, with the diversity and sheer numbers of organisms collected, separating and individually sequencing one of each kind is impossible. To get around this, a metagenomic approach is used where all the DNA from all the organisms collected on one filter are sequenced together in a pool. Afterwards, the genomes for each organism are sorted out and assembled computationally. Of course, this means it is not always possible to identify which genome comes from which organism. However, just the analysis of different gene variations in different organisms is incredibly revealing.

What Is the Tara Expedition Finding?

As the expedition just finished at the end of 2011, only a few results are available. Based on limited analysis from a few sites, however, it is clear that the diversity of the ocean is even greater than imagined. Initial DNA sequencing of ribosomal RNA, which every organism contains, has shown there appear to be over a million different types of marine protists globally. However, only tens of thousands of variants appear at each collection site. Comparing these site-to-site populations with the overall number of organisms collected suggests enormous diversity across the seas.

The Significance of the Marine Survey

Dr. Karsenti compares this undertaking to the sequencing of the human genome. In a way, maybe it is the sequencing of the ocean’s genome. It will certainly provide a massive amount of new genetic information—much more than just the single human genome did 12 years ago.

Based on initial DNA sequencing from a few collection sites, it appears about 90% of the genetic sequences are novel and not found in current sequence databases. Like the human genome, this data provides an immense resource for understanding how known genes work and finding new genes with novel functions. In addition to obviously expanding our comprehension of how earth's biosphere works, the analysis will inform developments in a range of areas, including basic biological research, bioremediation, agricultural improvement, and identifying new therapeutic targets and potential drugs. The Tara Oceans Expedition provides the basis for years of research uncovering new biological secrets devised by millions of years of evolution.

Global Warming and Marine Life

In addition to the long range scientific contributions, there is also a more immediate interest in understanding how changes in temperatures and ocean currents as a result of global warming will affect this very large segment of the biosphere. "Already," Dr. Karsenti noted, "it is known that plankton populations have moved north in the Atlantic and tropical fish are following them." While this is interesting, he pointed out that it is these one-celled microscopic organisms that have the most direct affect on the carbon dioxide and oxygen levels in the atmosphere. It is not simply how global warming will affect the diatoms and other one-celled marine organisms, but how the population and distribution changes of these organisms, which produce 20% of the oxygen in the atmosphere, will affect the rest of life on the planet.

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