Sequencing of Diatom Genome Highlights Genetic Diversity; “Transgenic by Nature”
17 October 2008
The diatom Phaeodactylum tricornutum. |
Diatoms have profound influence on the climate, producing 20% of atmospheric oxygen by capturing atmospheric carbon and in so doing, countering the greenhouse effect. An international team of researchers led by the US Department of Energy Joint Genome Institute (DOE JGI) and the Ecole Normale Supérieure of Paris have sequenced and analyzed the genome of the diatom Phaeodactylum tricornutum.
The researchers compared Phaeodactylum with the diatom Thalassiosira pseudonana, previously sequenced by DOE JGI, revealing a wealth of information about diatom biology, particularly the rapid diversification among the hundreds of thousands of diatom species that exist today.
The researchers found that the genetic structures of the two diatoms were dramatically different: 40% of their genes were not shared. Interestingly, the researchers found that hundreds of genes from bacteria were present in the genomes of both diatom species. The findings are published in 15 October edition of the journal Nature.
The bacterial genes found in diatoms could contribute to their success, enhancing their ability to perceive environmental signals or to metabolize organic carbon and nitrogen. Some of these bacterial genes might be responsible for certain cell-wall components in diatoms, and others for “unorthodox mechanisms of DNA replication, repair and recombination”. According to the study, “these findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans”.
These organisms represent a veritable melting pot of traits—a hybrid of genetic mechanisms contributed by ancestral lineages of plants, animals, and bacteria, and optimized over the relatively short evolutionary timeframe of 180 million years since they first appeared. Our findings show that gene transfer between diatoms and other organisms has been extremely common, making diatoms ‘transgenic by nature.’
—first author Chris Bowler of the Ecole Normale Supérieure
The study showed that gene transfer between diatoms and other organisms has been extremely common in marine environments. For example, the diatom inherited its photosynthetic capacity from plants, and its ability to process urea from animals (although unlike animals, diatoms use urea to store, not eliminate, nitrogen). The researchers propose that this gene transfer has been a major driving force during diatom evolution.
We believe this is the first time bacterial horizontal gene transfer has been observed in eukaryotes at such scale. This study gets us closer to explaining the dramatic diversity across the genera of diatoms, morphologically, behaviorally, but we still haven’t yet explained all the differences conferred by the genes contributed by the other taxa.
—senior author Igor Grigoriev of DOE JGI
The team documented more than 300 genes sourced from bacteria and found in both types of diatoms, pointing to their ancient origin and suggesting novel mechanisms of managing nutrients—for example utilization of organic carbon and nitrogen—and detecting cues from their environment.
Phaeodactylum was targeted for sequencing due to its value as a diatom model, given the ease with which it can be grown in the lab and the availability of tools to genetically transform it, and the comparisons with the previously sequenced diatom genome of Thalassiosira pseudonana.
Diatoms reside in fresh or salt water and can be divided into two camps, centrics and pennates. Pennates like Phaeodactylum look more like a cross between a boomerang and a narrow three-cornered hat—hence the species name, tricornutum. Not only is their shape and habitat diverse, so too is their behavior; for instance, the centrics get around by floating, the pennates by gliding through the water or on surfaces.
The lifestyle of diatoms can be characterized as “bloom or bust.” When light and nutrient conditions in the upper reaches of the ocean are favorable, particularly at the onset of spring, diatoms gain an edge and tend to dominate their phytoplankton brethren. When food is scarce, they die and sink, carrying their complement of carbon dioxide to the deeper recesses.
Bowler and his colleagues are also trying to understand the role that iron plays in the Phaeodactylum’s development. Iron is even more precious than nitrogen in the ocean and its absence in the southern hemisphere is likely a major cause of oceanic deserts of photosynthesis there. Bowler’s team has demonstrated that when iron deficiency occurs processes such as photosynthesis and nitrogen assimilation are suppressed.
Other studies, which hail diatoms as champions in capturing carbon dioxide, suggest a bold strategy of using iron as a fertilizer to provoke massive diatom blooms.
Once they have feasted, the weight of their silicon shells, which resemble glass, causes the diatoms to sink to the bottom of the ocean when they die, and the carbon that they assimilated is trapped there for millennia. By sequestering carbon in this way we could reverse the damage from the burning of fossil fuels
—Chris Bowler
The US Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories—Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the HudsonAlpha Institute for Biotechnology—to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup.
The collaboration included partners from 10 countries and was funded in part by the EU-funded DIATOMICS and Marine Genomics projects.
Resources
Bowler C., et al. (2008). The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. Published online 15 October; doi: 10.1038/nature07410
Seeding the oceans with iron could be a major mistake.. perhaps the current co2 levels are the only think keeping an ice age at bay.. a rapid uptake of co2 by diatoms could tip us over the edge..
Posted by: Herm | 17 October 2008 at 05:17 AM
I agree, let's kill all those diatoms.
Posted by: Anne | 17 October 2008 at 05:24 AM
Very tellingly, if raising the minute amounts of CO2 in the atmosphere were truly terrible in any way, this cheap solution would already be employed, whereby the oceans could have been seeded to stimulate the natural growth of plankton, with the missing trace minerals.
For the cost of conducting a single one of those interminable boondoggle "Conferences", to transport ten of thousands to Rio, Kyoto, Bali, or whatever exotic locations that all the government and quasi-government feeders at the public trough want to visit to merely hear once again how absolutely necessary it is for everyone ELSE to lower their standard of living.
Besides where is the Global Warming? It has stopped and been cooling for the past ten years. After the temperature climbed for but 19 years by tenths of a single degree and set off the orgy of hysteria.
Besides they have succeeded; it appears they will have elected the left wing socialist messiah, and it is necessary that the manufactured "problem" be cured by a wave of his magic tongue.
Posted by: stas peterson | 17 October 2008 at 08:10 AM
What r u saying Stas? That the potential for catastrophic climate destabilization is nonexistent? Is it just a "socialist" plot to undermine our "standard of living"? Does your theory relate to iron's effect on the ocean's ability to function as a carbon sink, or is it more of a theory of political science? Is it possible that you are just unhappy that American voters don't think Sarah Palin is ready for prime time? I hear she can see Russia from her kitchen window...
Posted by: Mick | 17 October 2008 at 09:52 AM
Edelman PR services: "If there was a problem with adding fossil fuel-sourced CO2 to the atmosphere, the algae would have dealt with it already."
Edelman won the American Petroleum Institute's $100 million PR contract, c. 2006, which was set up to counter the newly elected Congress' mandate to boost renewable energy and end government subsidies for fossil fuels. Their effort was largely successful - Big Oil and Big Coal retain all their tax breaks and subsidies, no meaningful climate legislation (fossil fuel caps) has been passed, or even discussed, and the meager existing renewable energy tax credits were almost defeated, until they were attached as a rider to the $700 billion financial bailout in order to help win the second House vote.
The API and the Edison Electric Institute (actually, the Coal-Fired Electricity Institute, but "edison" sounds better) are the two of the industry trade groups which, along with the U.S. Chamber of Commerce, are the leading financiers of the tobacco science PR blitz being run by various PR firms and front groups on the behalf of fossil fuel interests.
The actual science is very clear: fossil fuel CO2, in combination with deforestation, is raising the planet's surface temperature, leading to more water vapor in the atmosphere, which further raises the temperature. As a result, the oceans are warming, the Arctic has begun a rapid thaw (too be followed, within years or decades, by Antarctica), the world's mountain glaciers will be mostly gone within 20-80 years, and agriculture will suffer more frequent droughts, heat waves and other extreme weather events. That's just in the short term, too.
Well after we're all dead and gone, the world will be facing rising sea levels, drastically reduced agriculture capacity, acidic oceans, and massive extinction of species, some of which has already happened.
This will be bad for humans, but the diatoms will likely have few problems. However, there's plenty of evidence that algae won't draw down atmospheric CO2. That's because the vast majority of CO2 taken up by algae is later converted back to CO2 in the deep, oxygenated oceans.
If the depths of the oceans become stagnant and anoxic, then a large portion of algal photosynthesis-fixed carbon can indeed get buried - which is how most oil and gas deposits formed in the first place. However, the last time such large-scale carbon burial took place was tens to hundreds of millions of years ago.
These worst-case scenarios can be largely avoided by taking steps such as eliminating fossil fuels, halting and reversing deforestation, and using wind, sunlight and photosynthesis as the basis of the energy supply. That will require a less overconsumption-based economic system in the U.S. and globally, and that means the end of the most profitable business on the planet - the international fossil fuel trade.
The international slave trade might be the best analogy here - the slave-plantation society system worked, in a fashion, but was ultimately discredited and discarded. We don't need a slave-based economy, unlike what the pundits of the day argued, and we don't need a fossil-fuel based economy either.
Posted by: Ike Solem | 17 October 2008 at 10:49 AM
One of the predictions of the climate models is that increasing GHGs will warm the poles relative to the equator. That prediction has been a wild success.
Loss of both floating and grounded ice near both poles is on-going.Posted by: Reality Czech | 17 October 2008 at 11:07 AM
there is a link to a talk from 'bronze age astronomer' McCracken'
This fellow worked on ice core samples (hence bronze age) with reference to sun spot activity.
He writes in his book "Blast off"that he beleives that if here is no return to sunspot activity in the next six months, that we will likely be in for a 20 year extended cooling that will mask greenhouse increases.
He expresses concern that if this were to occur and people 'forget' the greenhouse gas contribution, that when sunspot activities resume , the problem will be compounded
http://www.abc.net.au/rn/scienceshow/stories/2008/2388008.htm
Posted by: arnold | 18 October 2008 at 01:42 PM
Climate has turned out to be a poor motivator for the goal of sustainable energy. The science is wobbly and average people cannot relate to expressions like 385ppm CO2 is melting the ice caps. It is in fact a PR issue. As Canada's recent election indicates - people don't care about climate, they care about their pocket books.
Ike pointed out, Energy is the greatest factor in nation-based and global economies. The transition to a diverse portfolio of non-fossil alternative energy will grow jobs, relieve international tensions and break the stranglehold energy monopolies (including electric utilities) hold over economies.
We've tried the Global Warming program for ten years with little result. It's time for a change (sound familiar?) and Global Energy Independence is the message that few disagree with. Put that message front and center and the world will follow. And without fighting, it'll fix climate.
Posted by: sulleny | 18 October 2008 at 02:28 PM
Climate change science is fairly sound and is supported by every recognized scientific organization. People very much care about the climate but it can be also said that the immediacy of the economic climate is very much a present situation.
The climate provides billions if not trillions of dollars worth of basically free services which everyone depends on. The loss of which would mean that we would have to divert resources to provide these services to ourselves.
Asking people to pay more for independence may make inroads to some but the protection of the environment and the loss of these valuable services is very real and hits much closer to a govt's home - their pocketbooks. Unfortuneately, to do something about it, requires them to hit their constituentes' pocketbooks. Additionally is the problem of the demonization over the years of the word environmentalism by extreme right.
Who has supported the developments that might possibly give greater independence? The hybrid and electric cars? Who has actually paid for the majority of them to this point? Who has weighed the opportunity costs available and paid for them and has laid the present foundations? It was the environmentalists.
Anyway, back to the diatoms. It is interesting to note though that diatoms may exibit different behaviours in different conditions. I'm not too sure though what this research will yield. The first commercialization of iron fertilization-carbon reduction failed. Do I expect different outcome in the future? Who knows. We may get some usefullness out of the genetic info but any information on the lifecycle of these organisms which contribute to the CO2/O2 cycle could be usefull especially in light of changing climate.
PS. Thanx for the info Ike. I was wondering if the renewable tax credit was ever going to get through the Senate with the Republican stalling tactics but with the present economic situation, god knows where the money will come from or even if the demand will be there. I will have to try to read up on the rider to the bill to see the specifics.
Posted by: aym | 19 October 2008 at 12:20 PM
It is safe to say that operative governments if not the entire race - deeply appreciate the vital, protective nature of our climate. It is clearly in the best interest of all to maintain the climate's integrity at the very highest level.
The question is how to BEST do this given the current levels of doubt and constraint. There appears to be no argument in the primary goal: an end to single point, fossil fuel-based energy. There are many very good reasons to support this. The climate model and AGW in particular has not resonated with the general public - who are needed to implement change. This has occurred in part because people have seen excessive stridency in climate mitigation. Debate, dialog, good people with differing (non-agenda) opinions have been hurt. Therein lie the roots of failure.
The goals in this pursuit (energy) are mutual and confirmed. How one goes about enlisting the human imagination to achieve them is open. One thing is certain, fear-based motivation is a detraction. It is our thought that a gradual, repositioning of message will enlist a far greater level of imagination. That reposition simply moves energy independence to the fore and quiets the immediacy of climate.
We certainly identify with environmentalists and their good work to improve the quality of life on Earth. While not quite in the Ansel Adams era - we can claim to be a founder of the Rachel Carson era. Energy independence at this stage of evolution is the single most effective guarantor of a clean environment. Billions of lives depend on it.
Posted by: sulleny | 19 October 2008 at 01:15 PM