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    The December 2008 issue of Tropical Conservation Science is now online. The issue features a special section on the conservation of Neotropical reptiles and amphibians as well as articles on the ecological impact of rural depopulation, conservation of manatees in southern Mexico, and co-management approaches to conservation in Tanzania. The next issue of Mongabay.com's open-access scientific journal will be published in March 2009. Tropical Conservation Science - December 09, 2008.

    Taiwan's Feng Chia University has succeeded in boosting the production of hydrogen from biomass to 15 liters per hour, one of the world's highest biohydrogen production rates, a researcher at the university said Friday. The research team managed to produce hydrogen and carbon dioxide (which can be captured and stored) from the fermentation of different strains of anaerobes in a sugar cane-based liquefied mixture. The highest yield was obtained by the Clostridium bacterium. Taiwan News - November 14, 2008.


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Thursday, December 11, 2008

From bioenergy to smart conservation

People come and go, and so do websites. With Biopact, we have tried to promote bioenergy in Africa as a way to help small farmers make a better living. We did so by pointing at possible strategies to use natural resources in as intelligent a manner as possible, and by connecting initiatives dealing with agriculture, forestry and bioenergy. We hinted at the role Europe could play by re-writing trade rules, farm subsidies and international development policies.

The small group of dedicated people who wrote for Biopact have learned a lot during these past few years. We learned, for example, that large-scale biofuel production may do a lot of harm, while small-scale, locally rooted bioenergy initiatives may change lives for the better. We gained an insight into new farming techniques, like biochar, which may help tackle key problems in the developing world. We changed perspectives when it became clear that the interrelated threats of climate change and energy insecurity require far more action on the part of individuals, communities and governments. And above all, we came to think that the few patches of untouched nature we have left on this planet, need to be conserved.

This is why we are pleased to refer our readers from now on to Mongabay - one of the most insightful resources on tropical conservation. Besides offering an overview of the latest in conservation science, Mongabay also tracks developments in the bioenergy sector, in climate change, and in the emerging markets for ecosystem services. It is one of the few resources which tries to go beyond classic contradictions and oppositions between conservation and development. Instead, Mongabay continuously explores ways to bridge this gap.

Meanwhile, the Biopact editors, writers and enthusiasts – who all worked as volunteers – move on to do other things. Some of us remain active in the bioenergy sector, while others plan to undertake entirely new adventures. We want to thank our readers for their loyalty, and hope they have gained as many insights into the topics we covered, as we have.

Signing off,-------Welcoming you,
The Biopact team------The Mongabay team

Article continues

Biochar to be considered as an official climate change mitigation and adaptation strategy

The International Biochar Initiative (IBI) announces that the United Nations Convention to Combat Desertification (UNCCD) has submitted a proposal to include biochar as a mitigation and adaptation technology to be considered in the post-2012-Copenhagen agenda of the UN Framework Convention on Climate Change (UNFCCC). The UNCCD proposal highlights the many benefits of biochar: the fact that it can be measured easily, the role it can play in sequestering carbon in dryland soils and its potential as a strategy to prevent deforestation.

Biochar is a fine-grained, highly porous charcoal that helps soils retain nutrients and water. The carbon in biochar resists degradation and can sequester carbon in soils for hundreds to thousands of years.

IBI Executive Director Debbie Reed said, "The UNCCD submission is a great success, and is paralleled by a lot of very positive discussions and interest in biochar amongst country delegates as well as observers of the process."

The UNCCD, a sister convention to the UNFCCC, has identified biochar as a unique opportunity to address soils as a carbon sink. According to the submission document:
The world's soils hold more organic carbon than that held by the atmosphere as CO2 and vegetation, yet the role of the soil in capturing and storing carbon dioxide is often one missing information layer in taking into consideration the importance of the land in mitigating climate change.
UNCCD proposes that biochar must be considered as a vital tool for rehabilitation of dryland soils: "The fact that many of the drylands soils have been degraded means that they are currently far from saturated with carbon and their potential to sequester carbon may be very high ... making the consideration of biochar, as a strategy for enhancing soils carbon sequestration, imperative."

UNCCD also cites the ability of biochar to address multiple climate and development concerns while avoiding the disadvantages of other bioenergy technologies that deplete soil organic matter (SOM).
Pyrolysis systems that produce biochar can provide many advantages. Biochar restores soil organic carbon and soil fertility, reduces emissions from agriculture, and can provide clean, renewable energy. Conventional biomass energy competes with soil building needs for crop residue feedstocks, but biochar accommodates both uses. - Debbie Reed, IBI Executive Director
Reduced deforestation is another biochar advantage cited by the UNCCD in their submitted proposal for including biochar in carbon trading mechanisms:
The carbon trade could provide an incentive to cease further deforestation; instead reforestation and recuperation of degraded land for fuel and food crops would gain magnitude.
UNCCD proposes to include biochar in the Clean Development Mechanism (CDM), and to revise the rules to account for biochar as a permanent means of carbon capture. UNCCD also proposes adjusting the carbon offset rules to allow greater financial flows to help developing countries increase soil organic matter with biochar.

Biochar has one important additional advantage over other land use carbon sequestration projects - carbon sequestration through biochar is easy to quantify. It is also relatively permanent.

The UNCCD says:
Potential drawbacks such as difficulty in estimating greenhouse gas removals and emissions resulting from land use, land use change and forestry (LULUCF), or destruction of sinks through forest fire or disease do not apply to biochar soil amendments.
Overall, the potential magnitude of biochar as a climate mitigation tool is great:
:: :: :: :: :: :: :: :: :: :: ::

IBI Board Chair Dr. Johannes Lehmann said, "We are pleased that the UNCCD has recognized the potential of biochar. Results from IBI's preliminary model to estimate the potential of biochar carbon sequestration show that biochar production from agriculture and forestry residues can potentially sequester one gigaton of carbon in the world's soils annually by 2040. Using the biochar energy co-product to displace fossil fuel energy can approximately double the carbon impact of biochar alone."

IBI's objective for the remainder of the UN meeting at Poznan is to interest more countries in proposing biochar for consideration as a mitigation and adaptation technology in the post-2012 Copenhagen process of the UNFCCC.

The International Biochar Initiative (IBI) is a registered non-profit organization that serves as an international platform for the exchange of information and activities in support of biochar research, development, demonstration and commercialization. IBI participants comprise a consortium of researchers, commercial entities, policy makers, development agents, farmers and gardeners and others committed to supporting sustainable biochar production and utilization systems that remove carbon from the atmosphere and enhance the earth's soils.

Many small scale initiatives are being launched to get biochar taken up by poor farmers in developing countries so that soils not only become carbon sinks, but yield more food and biomass. The activities of the Biochar Fund offer an interesting example. Its model is aimed at making biochar the kernel of a highly integrated development concept that succeeds in tackling food insecurity and low agricultural productivity amongst subistence farmers, deforestation, energy poverty and climate change - simultaneously.

Picture: seedlings illustrating the difference between plants grown in biochar-amended soil (darker soil on the right). Credit: Robert Flanagan.


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Africa proposes own solution to climate change: full range of bio-carbon sequestration actions


Africa has not benefited from the carbon markets even though it has a large potential to help win the fight against climate change. Now a large coalition of African countries calls for the inclusion of carbon credits generated from agriculture and forestry in future climate agreements. This was the key message behind a fresh and bold initiative launched at the COP 14 meeting in Poznan, Poland. The initiative aims to become a movement comprising all countries from the Global South, where most people make a living from agriculture. Poor farmers in developing countries have so far been excluded from climate negotiations. The coalition wants to change this, because these farmers bring many solutions to the table.

The African Climate Solution – the most ambitious initiative towards climate mitigation, adaptation and improved rural livelihoods for the continent – was launched in Poznan at the COP 14 meeting by a grouping of 26 African countries in East, Central and Southern Africa. The African Climate Solution entails the reduction of green house gas emissions by forest resources (REDD) and carbon sequestration through agriculture, forestry and land use (AFOLU) in Africa and throughout the developing world. Carbon sequestration can be achieved by activities such as reforestation, afforestation, agro-forestry, reduced tillage and biochar. The initiative intends to build a global coalition of developing countries into a "REDD-AFOLU Bio-carbon Coalition".
It is no longer a question of if or of when, Africa should be and will be part and parcel of a post–Kyoto Protocol regime. This initiative is African in origin but is intended to include all developing nations. We all face the same problem of dealing with climate change and sustainable development. We are seeking the support of countries in Asia, Latin America and Small Island States to ensure that not only Africa’s voice but that of the world’s poor and excluded will be heard loud and clear in articulating solutions for mitigation and adaptation measures on climate change. - Sindiso Ngwenya, Secretary General of COMESA
Africa is leading a high level delegation to Poznan comprising representatives from organisations representing farmers, the private sector, the research community, civil society development, partners and banks. The African Climate Solution initiative is a culmination of multi-sectoral and continent-wide consultations started in Johannesburg, South Africa in 2008.

According to the United Nations’ panel of climate experts, Africa is "highly vulnerable" to the impacts of climate change. Drivers include recurrent drought, degrading lands, and declines in agricultural productivity, and widespread poverty. Climate change has serious implications for economic growth, sustainable development and the achievement of the Millennium Development Goals (MDGs) as it magnifies, intensifies and speeds up already serious threats to ecosystems and the people.


Clean Development Mechanism (CDM) projects are concentrated in a handful of countries, and have largely bypassed Africa. Credit: UNFCCC/CDM.

The development gains attained in Africa are being threatened by the effects of global climate change, said Ngwenya, who has championed the call to use forest and agricultural systems to sustain Africa’s livelihoods. Over 100 developing nations have thus far received nothing from the global carbon markets because they are reliant on agriculture and forestry sectors which have been excluded from the current arrangements (see map of current CDM projects, click to enlarge).

The African Climate Solution calls for the expansion of eligibility of resources beyond REDD to include the full range of bio-carbon in the climate change negotiations. Agriculture, forestry, and land use all provide important opportunities for mitigating climate change and incentivising sustainable land use throughout the developing world.

Africa is calling for inclusion in the global carbon markets and the Clean Development Mechanisms of carbon credits for afforestation, reforestation, agroforestry, enhanced natural regeneration, re-vegetation of degraded lands, reduced soil tillage, and sustainable agricultural practices.
Despite the expansion of the global Market for Carbon emissions which the World Bank last year valued at over US$7.5 billion, Africa been left out in the cold. Most of all it excludes poor farmers. If they are included we can not only take the pressure off our existing forests the carbon market can help lift them out of poverty. - Sindiso Ngwenya
Africa’s civil society organisations (CSOs) have added their voice and endorsed the African Climate Solution as a model for a better future after 2012:
:: :: :: :: :: :: :: :: :: :: :: :: ::

All members of the Common Market for Eastern and Southern Africa (COMESA) have signed a declaration calling for the post Kyoto treaty to “include agriculture, sustainable land management, sustainable forest management, afforestation, reforestation reduced emissions from deforestation and forest degradation." This declaration is now also supported by The East African Community (EAC) and the Southern African Development Community (SADC)

Lead advocate for CSOs, Dr. Lindiwe Majele Sibanda, speaking at the launch, underlined the importance of global carbon market in transforming Africa’s agriculture and economies. "We are saying the carbon markets must reward our resource-poor farmers for contributing to efforts towards mitigating the effects of climate change,” said Dr. Sibanda, who is also CEO of the Food, Agriculture and Natural Resources Policy Analysis Network (FANRPAN), based in South Africa.
Africa has spoken with one voice on its readiness to join hands with the international community in securing a cleaner and sustainable planet for current and future generations. The time for that action is now. - Dr Sibanda
Africa has set the ball rolling, having developed a framework for the creation of an African Fund that would provide a sustainable carbon financing mechanism suitable for investments sustainable agriculture/agroforestry projects in Africa. The Fund will acquire offsets from African land-use projects on a large enough scale to channel meaningful streams of revenue to communities to ensure the successful implementation and on-going stewardship of land-use projects.

The initiative is supported and endorsed by leaders from the Global South like Bharrat Jagdeo (President of Guyana), Vincent Karega (Minister of Natural Resources from Rwanda), Catherine Namugala (Minister of Tourism, Environment, Natural Resources of Zambia), Rejoice Mabudafhasi (Deputy Minister of Environmental Affairs, South Africa), Agus Purnomo (Head of Indonesia’s National Council on Climate Change), Ligia de Doens (Minister of Environment for Panama), Blake (Ambassador of Antigua and Barbuda to the G77+China).

A number of international partners have endorsed the African Climate Solutions as well. Some of these include NEPAD, TerrAfrica, WWF, World Agroforestry Center, ICRAF, Terra Capital Global, International Food Policy Research Institute (IFPRI), the Food Association for Strengthening Agricultural Research in Eastern and (ASARECA) and Center for International Forestry Research (CIFOR).

Ahead of COP 15 in Copenhagen, the global climate change negotiations currently taking place in Poznan provide the best potential for Africa to formally contribute to climate change mitigation, adaptation, poverty eradication and sustainable development.

Article continues

Tuesday, December 09, 2008

FAO: number of hungry people rises to 963 million - economic crisis could compound woes

Another 40 million people have been pushed into hunger this year primarily due to higher food prices, according to preliminary estimates published by FAO today. This brings the overall number of undernourished people in the world to 963 million, compared to 923 million in 2007 and the ongoing financial and economic crisis could tip even more people into hunger and poverty, FAO warned.

World food prices have dropped since early 2008, but lower prices have not ended the food crisis in many poor countries, said FAO Assistant Director-General Hafez Ghanem, presenting the new edition of FAO's hunger report, The State of Food Insecurity in the World 2008.
For millions of people in developing countries, eating the minimum amount of food every day to live an active and healthy life is a distant dream. The structural problems of hunger, like the lack of access to land, credit and employment, combined with high food prices remain a dire reality. - Hafez Ghanem
Prices of major cereals have fallen by over 50 percent from their peaks earlier in 2008 but they remain high compared to previous years. Despite its sharp decline in recent months, the FAO Food Price Index was still 28 percent higher in October 2008 compared to October 2006 (graph 1, click to enlarge). With prices for seeds and fertilizers (and other inputs) more than doubling since 2006, poor farmers could not increase production. But richer farmers, particularly those in developed countries, could afford the higher input costs and expand plantings. As a result, cereal production in developed countries is likely to rise by at least 10 percent in 2008. The increase in developing countries may not exceed even one percent.

If lower prices and the credit crunch associated with the economic crisis force farmers to plant less food, another round of dramatic food prices could be unleashed next year, Ghanem added. The 1996 World Food Summit target, to reduce the number of hungry by half by 2015, requires a strong political commitment and investment in poor countries of at least $30 billion per year for agriculture and social protection of the poor.

Where the hungry live

The vast majority of the world's undernourished people - 907 million - live in developing countries, according to the 2007 data reported by the State of Food Insecurity in the World. Of these, 65 percent live in only seven countries: India, China, the Democratic Republic of Congo, Bangladesh, Indonesia, Pakistan and Ethiopia (graph 2, click to enlarge). Progress in these select countries with large populations would have an immediate and important impact on global hunger reduction.

On a side-note, it can be said that the situation in the DR Congo is almost unbearable: more than 75% of all Congolese are undernourished - the world's highest rate -, while the country has a large agricultural potential and could be a food exporter capable of meeting the needs of 2 to 3 billion people (previous post on the FAO's assessment and here). Clearly, food insecurity is not necessarily the result of a lack of agricultural potential:
:: :: :: :: :: :: :: :: ::

With a very large population and relatively slow progress in hunger reduction, nearly two-thirds of the world's hungry live in Asia (583 million in 2007). On the positive side, some countries in Southeast Asia like Thailand and Viet Nam have made good progress towards achieving the WFS target, while South Asia and Central Asia have suffered setbacks in hunger reduction.

In sub-Saharan Africa, one in three people - or 236 million (2007) - are chronically hungry, the highest proportion of undernourished people in the total population, according to the report. Most of the increase in the number of hungry occurred in a single country, the Democratic Republic of Congo, as a result of widespread and persistent conflict, from 11 million to 43 million (in 2003-05) and the proportion of undernourished rose from 29 to 76 percent.

Overall, sub-Saharan Africa has made some progress in reducing the proportion of people suffering from chronic hunger, down from 34 (1995-97) to 30 percent (2003-2005). Ghana, Congo, Nigeria, Mozambique and Malawi have achieved the steepest reductions in the proportion of undernourished. Ghana is the only country that has reached both the hunger reduction target of the World Food Summit and the Millennium Development Goals. Growth in agricultural production was key in this success.

Latin America and the Caribbean were most successful in reducing hunger before the surge in food prices. High food prices have increased the number of hungry people in the sub-region to 51 million in 2007.

Countries in the Near East and North Africa generally experience the lowest levels of undernourishment in the world. But conflicts (in Afghanistan and Iraq) and high food prices have pushed the numbers up from 15 million in 1990-92 to 37 million in 2007.

Almost out of reach
Some countries were well on track towards reaching the summit's target, before food prices skyrocketed but "Even these countries may have suffered setbacks - some of the progress has been cancelled due to high food prices. The crisis has mainly affected the poorest, landless and households run by women," Ghanem said. "It will require an enormous and resolute global effort and concrete actions to reduce the number of hungry by 500 million by 2015."

Exporters under threat
The world hunger situation may further deteriorate as the financial crisis hits the real economies of more and more countries. Reduced demand in developed countries threatens incomes in developing countries via exports. Remittances, investments and other capital flows including development aid are also at risk. Emerging economies in particular are subject to lasting impacts from the credit crunch even if the crisis itself is short-lived.

Picture
: The poorest, landless and female-headed households are hardest hit by high food prices. Credit: FAO.

References:

FAO: The State of Food Insecurity in the World 2008 - December 9, 2008.

Biopact: DR Congo debates its enormous biofuels potential - June 05, 2008

Biopact: UN's FAO: bright future for sustainable biofuels DR Congo - January 08, 2008



Article continues

Global warming aided by drought, deforestation link - carbon released by forest fires equal to fossil fuel emissions in equatorial Asia


In the rainforests of equatorial Asia, a link between drought and deforestation is fueling global warming, finds an international study. The analysis, focusing on six years of climate and fire observations from satellites, shows that in dry years, the practice of using fire to clear forests and remove organic soil increases substantially, releasing huge amounts of climate-warming carbon dioxide into the atmosphere.

In 2006, the climate on the fast-developing islands of Borneo and Sumatra and in New Guinea and other parts of equatorial Asia was three times drier than in 2000, but carbon emissions from deforestation were 30 times greater – exceeding emissions from fossil fuel burning.

Land managers respond to the drought by using fire to clear more land. In dry years, they burn deeper into the forest, which in turn releases more carbon dioxide, said James Randerson, climate scientist at UC Irvine and co-author of the study, published online the week of Dec. 8 in the Proceedings of the National Academy of Sciences.

The findings, Randerson says, illustrate why limits on deforestation should be a critical part of future climate agreements. Global warming modelers typically consider climate and land use separately when assessing how changes will affect greenhouse gas emissions:
:: :: :: :: :: :: :: :: :: ::

The results also indicate that forecasting drought may be important when countries in this region allocate resources to combat illegally set fires and clearing.

The link between drought and deforestation is very sensitive, Randerson said. If the climate warms and there are more droughts, it potentially makes the forest and its stored carbon more vulnerable.

Equatorial Asia is a hot spot for biodiversity but is undergoing widespread changes. Its global markets are growing, as is large-scale agricultural business. Forests and peatlands in the region store tremendous amounts of carbon, keeping it out of the atmosphere where it can turn into carbon dioxide and create warming.

The climate in equatorial Asia changes substantially from year to year and is linked with El Nino. Dry years occurred in 2002 and 2006; wet years in 2000 and 2005.

In a dry climate, fires are easier to set and burn more deeply into organic soil. When there is a lot of rainfall, fires don't burn as well, and it is more challenging to remove debris from areas that are being converted to agriculture, said Randerson, associate professor of Earth system science.

Randerson and his colleagues used several kinds of satellite data to develop and refine their emission estimates. First, they used satellite images of fire areas and additional information about carbon pools to estimate emissions from the region. Next, they sharpened their estimate using measurements of atmospheric carbon monoxide levels, which can be a strong signal of fire activity. In a final step, they used both carbon monoxide and satellite data to determine total carbon emissions.

Deforestation and carbon emissions are substantial and important contributors to the buildup of greenhouse gases in the atmosphere, Randerson said. "We should not neglect this flux in developing comprehensive approaches for stabilizing climate."


In addition to Randerson, scientists who collaborated on the study include G.R. van der Werf and A.J. Dolman of VU University Amsterdam; J. Dempewolf and D.C. Morton of the University of Maryland; S.N. Trigg of Cranfield University in the United Kingdom; P.S. Kasibhatla of Duke University; L. Giglio of Science Systems and Applications, Inc.; D. Murdiyarso of the Center for International Forestry Research in Indonesia; W. Peters of Wageningen University and Research Center in the Netherlands; G.J. Collatz of NASA Goddard Space Flight Center; and R.S. DeFries of Columbia University.

This work was supported by NASA and the Netherlands Organization for Scientific Research.

Picture
: A fire in a tropical peat forest on Sumatra in Indonesia. Credit: Florian Siegert.

References:

PNAS Article not yet online at time of release of this text.


Article continues

DOE Joint Genome Institute completes soybean genome — data released to advance biofuel, food, & feed research

The U.S. Department of Energy Joint Genome Institute (DOE JGI) has released a complete draft assembly of the soybean (Glycine max) genetic code, making it widely available to the research community to advance new breeding strategies for one of the world's most valuable plant commodities. Soybean not only accounts for 70 percent of the world's edible protein, but also is an emerging feedstock for biodiesel production. Soybean is second only to corn as an agricultural commodity and is the leading U.S. agricultural export.

DOE JGI's interest in sequencing the soybean centers on its use for biodiesel, a renewable, alternative fuel with the highest energy content of any alternative fuel. According to 2007 U.S. Census data, soybean is estimated to be responsible for more than 80 percent of biodiesel production.
The genome sequence is the direct result of a memorandum of understanding between DOE and USDA to increase interagency collaboration in plant genomics. We are proud to support this major scientific breakthrough that will not only advance our knowledge of a key agricultural commodity but also lead to new insights into biodiesel production. - Dr. Raymond L. Orbach, DOE Under Secretary for Science

Soybeans have been an important food plant providing essential protein to people for hundreds of years. Now, with the new knowledge available through this joint DOE/USDA genome sequencing project, researchers everywhere will be able to further enhance important traits that make the soybean such a valuable plant. It's a great day for agriculture and people everywhere. - Dr. Gale A. Buchanan, USDA Chief Scientist and Under Secretary for Research, Education, and Economics
The effort was led by Dan Rokhsar and Jeremy Schmutz of the DOE JGI, Gary Stacey of the University of Missouri-Columbia, Randy Shoemaker of the U.S. Department of Agriculture (USDA)-Agricultural Research Service (USDA-ARS), Scott Jackson of Purdue University, with support from the DOE, the USDA, and the National Science Foundation (NSF). In addition, the United Soybean Board, the North Central Soybean Research Program, and the Gordon and Betty Moore Foundation, have supported the soybean genome effort.

Soybean is the one of the largest and most complex plant genomes sequenced by the whole genome shotgun strategy, noted Rokhsar. The process entails shearing the DNA into small fragments enabling the order of the nucleotides to be read and interpreted. Steven Cannon of the USDA-ARS collaborated with the DOE team to ensure the accuracy of the assembly.

Preliminary scientific details emerging from the sequence analysis will be presented by Schmutz at the International Conference on Legume Genomics and Genetics in Puerto Vallarta, Mexico, December 8, 2008. The soybean genome sequence information can be browsed here.

Schmutz and colleagues have begun to analyze the soybean genome, which at one billion nucleotides is roughly one-third the size of the human genome. Preliminary studies suggest as many as 66,000 genes—more than twice the number identified in the human genome sequence, and nearly half-again as many as the poplar genome, sequenced by DOE JGI and published in the journal Science in 2006 (previous post).

We have ordered and localized about 5,500 genetic markers on the sequence, which promise to be of particular importance to those researchers seeking to optimize certain qualities in soybean, said Schmutz. Thousands of these markers were developed by Perry Cregan and colleagues of the USDA-ARS with support of the United Soybean Board. A genetic marker represents a known location on a chromosome that can be associated with a particular gene or trait. Prospective genome pathways of interest are those that directly influence yield, oil and protein content, as well as drought tolerance and resistance to nematodes and diseases such as the water mold Phytophthora sojae, previously sequenced by DOE JGI, which causes stem and root rot of soybean:
:: :: :: :: :: :: :: :: :: :: :: ::

In 2007, soybean accounted for 56 percent of the world's oilseed production. James Specht, Professor at the University of Nebraska, said that this nitrogen-fixing legume crop offers the dual benefit of a seed high in protein and oil—with room for improvement. With the advent of low-cost re-sequencing technologies, soybean scientists now have the means to identify sequence differences responsible for yield potential–the most desired of all crop traits, but to date the most intractable.

The soybean genome sequence will be a valuable resource for the basic researcher and soybean breeder alike, said Jim Collins, Assistant Director for the Biology Directorate at the NSF. Collins and Judith St. John of USDA Agricultural Research Service co-chair the Interagency Working Group on Plant Genomes, which oversees the National Plant Genome Initiative. The close coordination between the DOE sequencing project and the NSF SoyMap project facilitated through the National Plant Genome Initiative has added value to the sequence and physical map resources for this important crop, Collins said.

The soybean genome project is already making its mark out in the field.
It's tremendous that the soybean genome is out in the public's hands. Now every breeder can go into this valuable library for the information that will help speed up the breeding process. It should cut traditional breeding time by half from the typical 15 years. - Rick Stern, a New Jersey soybean farmer and chair of the Production Research program for the United Soybean Board (USB)
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five DOE 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. DOE JGI's Walnut Creek, Calif., Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

Picture: dried soybean pod. Credit: USDA/ARS/DOE JGI.


References:

DOE JGI: DOE Joint Genome Institute Completes Soybean Genome - December 8, 2008.

Previous DOE JGI sequencing efforts include:
Biopact: Scientists unveil genetics of plant-fungi symbiosis: boost to biomass for biofuels, carbon sequestration, phytoremediation - March 05, 2008

Biopact: Super-fermenting fungus genome sequenced, to be harnessed for biofuels - Monday, March 05, 2007

Biopact: Moss genome sequenced: shows how aquatic plants adapted to dry land - key to development of drought-tolerant energy crops, cellulosic biofuels - December 14, 2007

Biopact: Scientists sequence and analyse genomes of termite gut microbes to yield novel enzymes for cellulosic biofuel production - November 22, 2007

Biopact: The first tree genome is published: Poplar holds promise as renewable bioenergy resource - September 14, 2006

Biopact: Joint Genome Institute announces 2008 genome sequencing targets with focus on bioenergy and carbon cycle - June 12, 2007

Biopact: U.S. DOE to sequence the DNA of six photosynthetic bacteria to make biofuels - October 11, 2006

Biopact: DOE JGI releases soybean genome assembly to enable worldwide bioenergy research - January 18, 2008

Biopact: Forest genetics researchers to sequence and catalog conifer genes for future biofuels research - August 18, 2007




Article continues

Sunday, December 07, 2008

JCVI researchers streamline efficient construction of synthetic genomes - future biofuel applications

Researchers at the J. Craig Venter Institute (JCVI) have published a paper describing a significant advance in genome assembly in which the team can now assemble the whole bacterial genome, Mycoplasma genitalium, in one step from 25 fragments of DNA. The humble yeast Saccharomyces cerevisiae proves to be the ideal genetic factory for the process. Lead author Daniel G. Gibson, Ph.D. and his team published their results in the online early edition of the journal Proceedings of the National Academy of Sciences (PNAS).

The publication is another milestone in synthetic biology, a young branch of biotechnology that may one day help solve global problems like climate change, lead to new drugs, and generate hyper-efficient, 'endless' biofuels. Promising as it may be, the field is highly controversial and some civil society organisations demand a broader debate about the risks of synthetic biology (earlier post).

The new publication represents major improvements in the methods that the team developed and described in their January 2008 publication of the first synthesis of a bacterial genome, M. genitalium. That publication outlined how the team synthesized in the laboratory the 582,970 base pair M. genitalium genome using the chemical building blocks of DNA—adenine (A), guanine (G), cytosine (C) and thymine (T) (previous post).

While this was a big advance, it took several years to come to fruition and in the end was a tedious, multi- stage process in which the team had to build the genome a quarter at a time using the bacterium Escherichia coli to clone and produce the DNA segments. During this building process the team found that E. coli had difficulty reproducing the large DNA segments, so they turned to the yeast Saccharomyces cerevisiae. They were then able to finish creating the synthetic bacterial genome using a method called homologous recombination (a process that cells naturally use to repair chromosome damage).

Realizing how robustly yeast performed, the team wondered if it could be used to build the entire M. genitalium genome from multiple, smaller, overlapping segments of DNA. For this study the team used DNA fragments that ranged in size from about 17,000 base pairs to 35,000 base pairs. These relatively short segments were inserted into yeast cells in one step and through the mechanism of homologous recombination were assembled into the synthetic M. genitalium genome. Several experiments were then done to confirm that all 25 pieces of the synthetic DNA had been correctly assembled in the yeast cells, and to show that the experiment could be successfully reproduced.

The JCVI team continues to explore the capacity for DNA assembly in yeast, and the various applications of this particular method. They conjecture that a variety of combinations of DNA molecules and genetic pathways could be manufactured in yeast, in essence turning yeast into a genetic factory for specifically designed and optimized processes. This advance is being used by scientists at the company Synthetic Genomics Inc. in making next generation biofuels and biochemicals more efficiently:
:: :: :: :: :: :: :: ::
We continue to be amazed by the capacity of yeast to simultaneously take up so many DNA pieces and assemble them into genome-size molecules. This capacity begs to be further explored and extended and will help accelerate progress in applications of synthetic genomics. - Dr Gibson, lead author
Senior author Clyde Hutchison, Ph.D., adds that he is astounded by the team’s progress in assembling large DNA molecules. It remains to be seen how far they can push this yeast assembly platform but the team is hard at work exploring these methods as it works to "boot up" the synthetic chromosome.

The work was funded by the company Synthetic Genomics Inc. (SGI), which, among other things, has been active in studying the potential of synthetic genomics for applications in the biofuel sector (previous post).

Key Milestones
The JCVI builds on a portfolio of major scientific breakthroughs which gradually built up to the current status - a series of applications that may soon make the creation of artificial organisms possible:
Mid-1990’s: After sequencing the M. genitalium genome, Dr. Venter and colleagues begin work on the minimal genome project. This area of research, trying to understand the minimal genetic components necessary to sustain life, started with M. genitalium because it is a bacterium with the smallest genome known that can be grown in pure culture. This work was published in the journal Science in 1995.

2003: Drs. Venter, Smith and Hutchison (along with JCVI's Cynthia Andrews-Pfannkoch) made the first significant strides in the development of a synthetic genome by assembling the 5,386 base pair genome of bacteriophage ΦX174 (phi X). They did so using short, single strands of synthetically produced, commercially available DNA (known as oligonucleotides) and using an adaptation of polymerase chain reaction (PCR), known as polymerase cycle assembly (PCA), to build the phi X genome. The team produced the synthetic phi X in just 14 days.

2007: JCVI researchers led by Carole Lartigue, Ph.D., announced the results of work published in the journal Science, which outlined the methods and techniques used to change one bacterial species, Mycoplasma capricolum, into another, Mycoplasma mycoides Large Colony (LC), by replacing one organism’s genome with the other one’s genome. Genome transplantation was the first essential enabling step in the field of synthetic genomics as it is a key mechanism by which chemically synthesized chromosomes can be activated into viable living cells.

January 2008: The second successful step in the JCVI teams’ journey to create a cell controlled by synthetic DNA was completed when Gibson et al published in the journal Science, the synthetic M. genitalium genome. The team is still working on experiments to install a fully synthetic bacterial chromosome into a recipient cell and thus “boot up” a synthetic chromosome.
Ethical Considerations
Since the beginning of the quest to understand and build a synthetic genome, Dr. Venter and his team have been concerned with the societal issues surrounding the work. In 1995 while the team was doing the research on the minimal genome, the work underwent significant ethical review by a panel of experts at the University of Pennsylvania (Cho et al, Science December 1999:Vol. 286. no. 5447, pp. 2087 – 2090). The bioethical group's independent deliberations, published at the same time as the scientific minimal genome research, resulted in a unanimous decision that there were no strong ethical reasons why the work should not continue as long as the scientists involved continued to engage public discussion.

Dr. Venter and the team at JCVI continue to work with bioethicists, outside policy groups, legislative members and staff, and the public to encourage discussion and understanding about the societal implications of their work and the field of synthetic genomics generally. As such, the JCVI’s policy team, along with the Center for Strategic & International Studies (CSIS), and the Massachusetts Institute of Technology (MIT), were funded by a grant from the Alfred P. Sloan Foundation for a 20-month study that explored the risks and benefits of this emerging technology, as well as possible safeguards to prevent abuse, including bioterrorism. After several workshops and public sessions the group published a report in October 2007 outlining options for the field and its researchers.

This report was criticized by a number of organisations, who demand a far broader debate about the potential benefits and risks of synthetic biology (previous post).


Illustration: Assembly of the synthetic M. genitalium genome in yeast from 25 overlapping DNA fragments. Credit: J. Craig Venter Institute.

References:

Biopact: Scientists create first synthetic bacterial genome - importance for biofuels - January 25, 2008

Biopact: Civil society organizations respond to report on synthetic biology governance - October 18, 2007


Biopact: Scientists take major step towards 'synthetic life': first bacterial genome transplantation changing one species to another - June 29, 2007

Biopact: Breakthrough in synthetic biology: scientists synthesize DNA-based memory in yeast cells, guided by mathematical model - September 17, 2007

Biopact: Scientists call for global push to advance synthetic biology - biofuels to benefit - June 25, 2007

Biopact: Scientists patent synthetic life - promise for 'endless' biofuels - June 09, 2007

Biopact: Synthetic Genomics and Asiatic Centre for Genome Technology to sequence oil palm genome - July 11, 2007

Biopact: Agrivida and Codon Devices to partner on third-generation biofuels - August 03, 2007

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