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International team sequences Eucalyptus genome; potential for improving biofuel and biomaterial production

14 June 2014

An international team of researchers has sequenced the genome of the eucalyptus tree (Eucalyptus grandis) and published the analysis in an open access paper in the journal Nature. With its prodigious growth habit, the eucalyptus tree, one of the world’s most widely planted hardwood trees, has the potential to enhance sustainable biofuels and biomaterials production, and to provide a stable year-round source of biomass that doesn’t compete with food crops.

The researchers reported the sequencing and assembly of more than 94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes, which can be substituted catalytically for jet fuel.

By having a library of these genes that control the synthesis of terpenes we are able to dissect which genes produce specific terpenes; then we can modify this biochemical pathway in the leaves so that we can develop the potential of Eucalyptus as an alternative source feedstock for jet fuel.

—Gerald Tuskan, Oak Ridge National Laboratory

The international effort to sequence and analyze the genome of Eucalyptus grandis engaged more than 80 researchers from 30 institutions, representing 18 countries. The project was led by Alexander Myburg of the University of Pretoria (South Africa); Dario Grattapaglia of the Brazilian Agricultural Research Corporation (EMBRAPA) and Catholic University of Brasilia; Gerald Tuskan of the Oak Ridge National Laboratory and the BioEnergy Science Center and US Department of Energy Joint Genome Institute (DOE JGI); Dan Rokhsar of the DOE JGI and Jeremy Schmutz of the DOE JGI and the HudsonAlpha Institute for Biotechnology.

“A major challenge for achieving a sustainable energy future is our understanding of the molecular basis of superior growth and adaptation in woody plants suitable for biomass production.”
—Alexander Myburg

Trees play a significant role in the global carbon cycle. Collectively, they represent a major terrestrial repository of carbon and play both active CO2 capture and processing and passive storage roles. With these advantages in mind, Eucalyptus can be harvested from tropical and temperate zones and has more than 700 species that are rich in genetic variation.

Because of its wide adaptability, extremely fast growth rate and excellent wood and fiber properties, Eucalyptus trees, while native to Australia, are grown in 100 countries across six continents and account for over 40 million acres. Eucalyptus trees are planted worldwide mostly for the value of its wood; for the Department of Energy, their energy-rich cellulosic biomass makes them one of the principal candidate biomass energy crops.

Combing through the 36,000-plus genes found in Eucalyptus (nearly twice as many as in the human genome), the researchers homed in on those that may influence the production of secondary cell wall material that can be processed for pulp, paper, biomaterials and bioenergy applications.

Approximately 80% of the woody biomass in a Eucalyptus is made of cellulose and hemicellulose, both long chains of sugars, with the remaining biomass primarily comprised of lignin.

We have a keen interest in how wood is formed. A major determinant of industrial processing efficiency lies in the composition and cross-linking of biopolymers in the thick secondary cell walls of woody fibers. Our analysis provides a much more comprehensive understanding of the genetic control of carbon allocation towards cell wall biopolymers in woody plants—a crucial step toward the development of future biomass crops.

—Gerald Tuskan

Our comparative analysis of the complex traits associated with the Eucalyptus genome and other large perennials offers new opportunities for accelerating breeding cycles for sustainable biomass productivity and optimal wood quality. In addition, insights into the trees’ evolutionary history and adaptation are improving our understanding of their response to environmental change, providing strategies to diminish the negative environmental impacts that threaten many species.

—Dario Grattapaglia

The eucalyptus team identified genes encoding 18 final enzymatic steps for the production of cellulose and the hemicellulose xylan, both cell wall carbohydrates that can be used for biofuel production.

By tracing their evolutionary lineages and expression in woody tissues we defined a core set of genes as well as novel lignin-building candidates that are highly expressed in the development of xylem—the woody tissue that helps channel water throughout the plant—which serves to strengthen the tree.

—Alexander Myburg

The team’s detailed analysis of the Eucalyptus genome revealed an ancient whole-genome duplication event estimated to have occurred about 110 million years ago, as well as an unusually high proportion of genes in tandem duplicate arrays. Their results, Tuskan said, highlight the major role of the phenomenon of tandem replication in shaping functional diversity in Eucalyptus and suggest that Eucalyptus may have followed an evolutionary path that highlighted specific genes for woody biomass production.

By comparison, Eucalyptus has three times the number of tandem repeat genes present in poplar, the first tree sequenced (by the DOE JGI and published on the cover of the journal Science in 2006).

The genetic architecture of inbreeding depression, often referred to as the converse of hybrid vigor, is largely unknown for trees and was also tackled in the study.

This poses a barrier to their rapid domestication and breeding improvements by way of self-pollination. Our results in Eucalyptus suggest that cumulative effects of many small genetic variants throughout the genome are responsible for these fundamental genetic phenomena. Favorably combined, they determine the height of a tree, which is one of our gauges for overall fitness.

—Dario Grattapaglia

The extensive catalog of genes contributed by the team will allow breeders to adapt Eucalyptus trees for sustainable energy production in regions, such as the US Southeast, where it cannot currently be grown.

The Eucalyptus genome data are available publicly through the DOE JGI’s comparative plant genomics portal known as Phytozome, now in its 10th revision.

Resources

  • Alexander A. Myburg, Dario Grattapaglia, Gerald A. Tuskan, Uffe Hellsten, Richard D. Hayes, Jane Grimwood, Jerry Jenkins, Erika Lindquist, Hope Tice, Diane Bauer, David M. Goodstein, Inna Dubchak, Alexandre Poliakov, Eshchar Mizrachi, Anand R. K. Kullan, Steven G. Hussey, Desre Pinard, Karen van der Merwe, Pooja Singh, Ida van Jaarsveld, Orzenil B. Silva-Junior, Roberto C. Togawa, Marilia R. Pappas, Danielle A. Faria, Carolina P. Sansaloni et al. (2014) “The genome of Eucalyptus grandis,” Nature doi: 10.1038/nature13308

June 14, 2014 in Bio-hydrocarbons, Biomass, Biotech, Fuels | Permalink | Comments (24) | TrackBack (0)

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"..biomass that doesn’t compete with food crops."

Some will always complain that they compete for land and water. That is why I advocate making synthetic biofuels using corn stalks and wheat straw. We grow the crops anyway for food, use the stalks for fuel. No extra land nor water required.

Eucalypts are invasive species and do not support native wildlife; they were a major factor in the wildfires which hit SoCal in the early 80's.

Eucalypts are a native species and support native wildlife. Depends on where you live.

Of course the question is, do they support biofuels.

Apparently they do - and can be made better.

But my car is apprehensive of GMOs.

Since we have enough Oil and NG for 54+ and 92+ years respectively, at the current burning-combustion rate, wouldn't it be more appropriate to:

1. continue to use fossil fuels but use cleaner and more efficient combustion methods to reduce GHG and pollution and/

2. progressively switch to hybrid and electrified vehicles (HEVs, PHEVs, BEVs and FCEVs, e-trains, small e-planes etc) to wean ourselves of burning-combustion fuels and/

3. avoid using productive land, water and polluting the environment with production and combustion of bio-fuels and/

4. produce clean e-fuels for airplanes.

sure, run hybrids on bio synthetic fuels that are CO2 neutral. We reduce fossil fuel use, reduce imported oil and clean the air. Nothing to it, but to DO it.

Which bio-fuel is really 100% CO2 neutral and is fully non-polluting? Certainly not corn ethanol.

Very soon we will convert cellulose to food, instead of food to fuel.
Production of biomass through trees/large grasses is much more productive and ecological than through conventional food crops.
Technologies like those from solazyme and others will produce proteins, starches and lipids in amounts unimaginable through normal agriculture, and with much less water use, fossil fuel use, and chemicals.
These foods will also be more healthy and tasty and cheaper.
Just let the free market deside.

"I advocate making synthetic biofuels using corn stalks and wheat straw"
--> Not a good idea IMHO as this depletes the soil’s organic matter slowly killing it resulting in reduced yields. http://en.wikipedia.org/wiki/Soil#Organic_matter

"Just let the free market deside."
-> OK as long as externalities are priced and paid for by those generating them…

Recent studies have shown that you can use HALF of the corn stalks and wheat straw with NO adverse affects on the land. We make a fuel that is more CO2 neutral than fossil fuels.

All too often people come up with reasons we can not or should not do something and believe it even when they are wrong. Many will say it must satisfy ALL our fuel needs or forget it. Faulty thinking has always impeded progress.

http://www.fuelinggrowth.org

During the pyrolysis of waste biomass into bio-crude oil, some biochar will be formed. The following from Wikipedia:

"Biochar is a name for charcoal when it is used for particular purposes, especially as a soil amendment. Like all charcoal, biochar is created by pyrolysis of biomass. Biochar is under investigation as an approach to carbon sequestration to produce negative carbon dioxide emissions.[1][dead link] Biochar thus has the potential to help mitigate climate change, via carbon sequestration. [2] [3] Independently, biochar can increase soil fertility, increase agricultural productivity, and provide protection against some foliar and soil-borne diseases. Furthermore, biochar reduces pressure on forests.[4] Biochar is a stable solid, rich in carbon and can endure in soil for thousands of years.[1]"

THe following quote gives some insight into the pyrolysis process of waste biomass:

"Pyrolysis produces biochar, liquids, and gases from biomass by heating the biomass in a low/no oxygen environment. The absence of oxygen prevents combustion. The relative yield of products from pyrolysis varies with temperature. Temperatures of 400–500 °C (752–932 °F) produce more char, while temperatures above 700 °C (1,292 °F) favor the yield of liquid and gas fuel components.[10] Pyrolysis occurs more quickly at the higher temperatures, typically requiring seconds instead of hours. High temperature pyrolysis is also known as gasification, and produces primarily syngas.[10] Typical yields are 60% bio-oil, 20% biochar, and 20% syngas. By comparison, slow pyrolysis can produce substantially more char (~50%). Once initialized, both processes produce net energy. For typical inputs, the energy required to run a “fast” pyrolyzer is approximately 15% of the energy that it outputs.[11] Modern pyrolysis plants can use the syngas created by the pyrolysis process and output 3–9 times the amount of energy required to run.[6]"

When renewable-energy H2 will be added during the pyrolysis process in the presence of appropriate catalysts, a bio-crude oil chemically similar to petroleum crude oil can result which can be transported via pipelines to refineries to produce transportation fuels. The fuel yield with the addition of H2 can double, thus allowing renewable energy from solar, wind, hydro, etc. to be converted to liquid hydrocarbon fuels at low cost and high efficiency. With more H2 addition, synthetic biomethane can be made and can triple the energy yield for a given amount of carbon incorporated within the waste biomass.

It is not a good idea to leave the cellulose to rot in the field because other organisms to convert or ferment these into methane which has very high GHG index, or into CO2, which we do not want to release. Instead, putting biochar back into the soil can serve dual roles as carbon sequestration and soil enrichment.

If we're going to tie up carbon, maybe organic carbon plus powdered olivine (or other alkalai-earth silicate) is indicated.  If the carbon released by decomposers reacts with magnesium or calcium to form carbonate, it is also sequestered.

I'd love to see what research has to say about this.

Goods points RP. Maybe, China with faster growing bamboo and eucalyptus could produce some of the essential fuels, gas and chemicals required for their very fast growing industry while reducing GHGs?

HarveyD,

We already are progressively to hybrid and electrified vehicles. The problem is that we aren't doing it fast enough. While you claim that we have 54+ years of oil reserves left, that number could be a little higher (not likely) or much lower (more likely given the incentives to overstate reserves since they act much like money in the bank that can be used to leverage other financial transactions.)

And regardless of how much oil is still left in the ground, it's not like we'll approach 2068 and have a nice, gentle glide-path down to zero oil production. It takes decades to make the transition off fossil fuels and giving ourselves a false sense of security by thinking there are many decades of oil production left means that we will lock ourselves into ever more oil consumption as we ignore the problem. Meanwhile, the atmosphere gets loaded with more and more CO2 and we'll have to endure the economic shocks and human tragety associated with worsening climate change. At the same time, other countries will be increasing their oil consumption as well, tightening the supply and making oil prices much more volitale. As the price of oil inches higher, more and more money will flow into the pockets of despots in Russia, Iraq, Iran, Nigeria and other countries blessed with the "resource curse".

I agree, using valuable land and water to grow biofuels that might not be all that effective at really solving our problems is a dead end. However, using oil at our current clip will not give us 54+ years of smooth sailing and dealing with the problems it causes will be so expensive, people will run the numbers and figure out it was probably a better idea for the government to just buy everybody an electric car and be done with this oil nonsense.

@ sault.

I'm not at all pro fossil fuels (coal, oil or NG) but they exist, are relatively very cheap and the world need most of it to maintain higher growth rates.

To vote a complete ban on fossil and bio fuels burning-combustion would be suicidal for any politician who would dare do it and it (the ban and the politician) would be rather short lived.

A progressive fossil and bio fuels combustion reduction and associated CO2 emissions is possible. A compromise solution would include but not be restricted to the following solutions:

1. CPPs and NGPPs can be cleaned up with CO2 and pollution capture.

2. Most ICEVs efficiency can be further increased to over 100 mpg to reduce liquid fuels usage and associated GHGs.

3. Current and future HEVs, PHEVs, BEVs and FCEVs can further reduce liquid fuels consumption and GHGs.

4. Adding a progressive pollution tax on combustion fuels (coal, oil, bio-fuels and NG) could promote and accelerate the sale of clean electrified vehicles and clean electricity production and storage.

By reducing consumption of fossil fuels (and bio-fuels), the world reserves would last 100+ years and GHGs would be spread over another century or so.

Which would be just as fatal to the biosphere; GHGs take 1000 years to equilibrate with the oceans, and 1 million years to stabilize with weathering.

What the world needs is an immediate push for nuclear energy to replace essentially all combustion-driven electric generation, the electrification of nearly all transport and industry, and the creation of carbon sinks as part and parcel of new processes.  The atmospheric CO2 level must be returned to the neighborhood of 350 ppm.  Otherwise our coasts will become distant memories and Sandy and Haiyan are just the beginning.

@Harvey,
Wise politicians would not ban fossil fuels right away, because right now, there is not enough alternative sources to replace them. However, what need to be done is a comprehensive program involve development of all non-CO2 energy sources like RE and nuclear along with electrification of transportation, parallel with a waste biomass synthetic fuel program that can combine the RE-H2 with the waste biomass with the capacity of eventually replacing all fossil fuel sources.

With these kind of program in place, the politicians will be able to announce in advance the time table for the start of carbon tax to be phased in gradually in 5-10 years from now. I repeat: NOT NOW, only after 5-10 years, in order to ensure PRIVATE investments into these synthetic fuel program in anticipation of future action. The carbon tax will be phase-in so gradually that no disruption to the economy will result, but instead, the economy will BOOM, due to all the investments and job creation into GREEN ENERGY. Once synthetic fuels and CO2-free energy will be available at cost parity with fossil fuels, then no one will object to carbon tax.

In this scenario, the politicians will want to take credit for the job creation during the transition toward 100% fossil-fuel free and so will want to be the ones that voted for the future carbon tax along with the rest of the plan to make the carbon tax feasible, just like Pres. Obama voted NO for the Iraq war and thus got elected.

Within 10 to 15 years, Alberta's Tar Sands will produce up to 6.5 million barrels/day. Less than 50% will be consumed (burned) in Canada and the other 50% will be exported to USA, Asia and EU.

The total GHGs (sands to wheels) produced will still be very high.

Meanwhile, more dirty lower cost CPP plants will be built and the current 2000 or so units will continue to pollute.

CPPs and ICEVs will continue to increase CO2 level from 404 ppm to close to 450 ppm.

USA, Canada, Australia will still be the highest per capita polluters. China's and India's will rise but not reach our high per capita level.

Short of a progressive carbon tax, we may not wean ourselves from cheap combustible (fossil or bio) fuels until we have burnt the last drop or have not enough land to produce alternative combustible fuels or we have damaged the planet beyond repair.

Nobody knows which will come first?

Good point, HarveyD.

The world will continue to use fossil fuels because of the inertia and the high upfront cost of investment into RE and nuclear energy. However, once the investments are made to produce RE like solar and wind, RE and synthetic fuels produced from RE will prove to cost less than petroleum, while costing on par with Natural gas (NG) and coal, and will displace the use of fossil fuels.

The trick is how to induce rapid investments into RE collectors, transmission lines, and synthetic fuel production facilities.

One way to do it is for the USA and NATO to declare WAR on GLOBAL WARMING (GW). This will unleash at least 1/2 of the US and NATO defense budgets to fund these RE projects. All defense contractors as well as military personnel will be invited to participate, thus will guarantee easy
Congressional support. The Oil and Gas industry will be invited to participate as well, to set up facilities for gathering waste biomass and for production of crude bio-oil, using some of the money earmarked for the WAR on GW. Again, easy Congressional approval, due to the strong influence of these folks in our Govt.

With gov. money invested into the production of RE and synthetic fuels, you will see that the final products will cost a lot less than fossil fuels, because these non-fossil-fuel energy sources are heavily subsidized using Defense budget. Oil companies will stop investing into oil and gas drilling with their own money, when they can use US and NATO defense money to build up facilities for synthetic fuels.

These are the "carrots". Now comes the "stick" of the "Carrot and stick" method: Announce in advance the time table for commencement of the Carbon Tax...not now, but in due time, 7-15 years or more, when there will be sufficient production of RE and synthetic fuels...Thus, when will come the Carbon Tax, NO ONE will suffer from it, because RE and synthetic fuels will be more plentiful and cheaper than previous fossil fuels even before tax.

RE is a very expensive boondoggle; Ontario's electric prices are due to double after the Liberal party's failed push for "green" power made little power but large bills to pay.  Ontario has de-carbonized its electricity a second time by refurbishing its nuclear fleet; Denmark, despite having huge interconnection capacity to hydro-heavy Norway and Sweden, has multiples of Ontario's per-kWh carbon emissions.  Nuclear, not "renewables", is the only workable way forward.

Nuclear for base load power, Hydro for peak load while solar for peak summer load, wind for nightly charging of PEV's, and excess of nuclear, solar, and wind for production of synthetic fuels. Every non-fossil-fuel energy source has important roles to play.

Nuclear is best for locations not rich in RE, while Hydro and geothermal are great wherever the resources are available. HVDC power lines can be used to even out the continental grid, however, due to the cost and energy security issue involved such as vulnerability to terrorist attack, should not be used for transmission of 100% of power demand of a region. Each region should have its own generation capacity, including synthetic fuel reserve for backing up RE sources.

Due to the limit availability of nuclear engineers, technicians and workers and nuclear fuel resources, RE should be developed in parallel with nuclear energy development in order to stop the GW runaway train to avert disasters. Without the storage requirement, RE's cost is on par with fossil fuels, and RE is ideal energy source for the production of synthetic fuels (H2, synthetic methane and gasoline and diesel).

Fast rising initial and rehab cost, extremely high nuclear waste elimination cost and growing lack of public acceptance will delay or block future NPPs.

CPPs could pollute the planet out of existence.

NGPPs may be the lesser of both evils but still pollute too much.

Hydro is excellent but limited in many places.

Solar and Wind are renewable, affordable, almost unlimited and will supply a greater part of the electricity needed in the coming decades. Appropriate storage will make those two sources available 24/7. Distributed generation make them more secure than large centralized CPPs, NGPPS and NPPs.

The proper choice will be rather easy to make.

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