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    At the 148th Meeting of the OPEC Conference, the oil exporting cartel decided to leave its production level unchanged, sending crude prices spiralling to new records (above $104). OPEC "observed that the market is well-supplied, with current commercial oil stocks standing above their five-year average. The Conference further noted, with concern, that the current price environment does not reflect market fundamentals, as crude oil prices are being strongly influenced by the weakness in the US dollar, rising inflation and significant flow of funds into the commodities market." OPEC - March 5, 2008.

    Kyushu University (Japan) is establishing what it says will be the world’s first graduate program in hydrogen energy technologies. The new master’s program for hydrogen engineering is to be offered at the university’s new Ito campus in Fukuoka Prefecture. Lectures will cover such topics as hydrogen energy and developing the fuel cells needed to convert hydrogen into heat or electricity. Of all the renewable pathways to produce hydrogen, bio-hydrogen based on the gasification of biomass is by far both the most efficient, cost-effective and cleanest. Fuel Cell Works - March 3, 2008.


    An entrepreneur in Ivory Coast has developed a project to establish a network of Miscanthus giganteus farms aimed at producing biomass for use in power generation. In a first phase, the goal is to grow the crop on 200 hectares, after which expansion will start. The project is in an advanced stage, but the entrepreneur still seeks partners and investors. The plantation is to be located in an agro-ecological zone qualified as highly suitable for the grass species. Contact us - March 3, 2008.

    A 7.1MW biomass power plant to be built on the Haiwaiian island of Kaua‘i has received approval from the local Planning Commission. The plant, owned and operated by Green Energy Hawaii, will use albizia trees, a hardy species that grows in poor soil on rainfall alone. The renewable power plant will meet 10 percent of the island's energy needs. Kauai World - February 27, 2008.

    Tasmania's first specialty biodiesel plant has been approved, to start operating as early as July. The Macquarie Oil Company will spend half a million dollars on a specially designed facility in Cressy, in Tasmania's Northern Midlands. The plant will produce more than five million litres of fuel each year for the transport and marine industries. A unique blend of feed stock, including poppy seed, is expected to make it more viable than most operations. ABC Rural - February 25, 2008.

    The 16th European Biomass Conference & Exhibition - From Research to Industry and Markets - will be held from 2nd to 6th June 2008, at the Convention and Exhibition Centre of FeriaValencia, Spain. Early bird fee registration ends 18th April 2008. European Biomass Conference & Exhibition - February 22, 2008.

    'Obesity Facts' – a new multidisciplinary journal for research and therapy published by Karger – was launched today as the official journal of the European Association for the Study of Obesity. The journal publishes articles covering all aspects of obesity, in particular epidemiology, etiology and pathogenesis, treatment, and the prevention of adiposity. As obesity is related to many disease processes, the journal is also dedicated to all topics pertaining to comorbidity and covers psychological and sociocultural aspects as well as influences of nutrition and exercise on body weight. Obesity is one of the world's most pressing health issues, expected to affect 700 million people by 2015. AlphaGalileo - February 21, 2008.

    A bioethanol plant with a capacity of 150 thousand tons per annum is to be constructed in Kuybishev, in the Novosibirsk region. Construction is to begin in 2009 with investments into the project estimated at €200 million. A 'wet' method of production will be used to make, in addition to bioethanol, gluten, fodder yeast and carbon dioxide for industrial use. The complex was developed by the Solev consulting company. FIS: Siberia - February 19, 2008.

    Sarnia-Lambton lands a $15million federal grant for biofuel innovation at the Western Ontario Research and Development Park. The funds come on top of a $10 million provincial grant. The "Bioindustrial Innovation Centre" project competed successfully against 110 other proposals for new research money. London Free Press - February 18, 2008.


    An organisation that has established a large Pongamia pinnata plantation on barren land owned by small & marginal farmers in Andhra Pradesh, India is looking for a biogas and CHP consultant to help research the use of de-oiled cake for the production of biogas. The organisation plans to set up a biogas plant of 20,000 cubic meter capacity and wants to use it for power generation. Contact us - February 15, 2008.

    The Andersons, Inc. and Marathon Oil Corporation today jointly announced ethanol production has begun at their 110-million gallon ethanol plant located in Greenville, Ohio. Along with the 110 million gallons of ethanol, the plant annually will produce 350,000 tons of distillers dried grains, an animal feed ingredient. Marathon Oil - February 14, 2008.


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Wednesday, March 05, 2008

Scientists unveil genetics of plant-fungi symbiosis: boost to biomass for biofuels, carbon sequestration, phytoremediation

Plants gained their ancestral toehold on dry land with considerable help from their fungal friends. Now, millennia later, that partnership is being exploited as a strategy to bolster biomass production for next generation biofuels. The genetic mechanism of this kind of symbiosis, which contributes to the delicate ecological balance in healthy forests, provides insights into plant health that may enable more efficient carbon sequestration ('fourth generation' carbon-negative bioenergy systems) as well as enhanced phytoremediation, using plants to clean up environmental contaminants.

These prospects stem from the genome analysis of the symbiotic fungus Laccaria bicolor, generated by the U.S. Department of Energy Joint Genome Institute (DOE JGI) and collaborators from INRA, the National Institute for Agricultural Research in Nancy, France, and published March 6 in the journal Nature.

This international team effort also involved contributions from more than 60 scientists from 16 institutions, including Oak Ridge National Laboratory; Ghent University, Belgium; Lund University, Sweden; Goettingen University, Germany; CNRS-Aix-Marseille University, France; Nancy University, France; and the University of Alabama, Huntsville. The international collaboration is part of a world-wide effort to research the genomes of all organisms involved in current and future bioenergy systems: from genomic information about bacteria to biomass crops, from fungi to soil microbes and exotic extremophiles.

Trees' ability to generate large amounts of biomass or store carbon is underpinned by their interactions with soil microbes known as mycorrhizal fungi, which excel at procuring necessary, but scarce, nutrients such as phosphate and nitrogen. Most of these nutrients are transferred to the growing tree. When Laccaria bicolor establishes a partnership with plant roots, a mycorrhizal root is created. The fungus within the root is protected from competition with other soil microbes and gains preferential access to carbohydrates within the plant. Thus, the mutualistic relationship is established.
Forests around the world rely on the partnership between plant roots and soil fungi and the environment they create, the rhizosphere. The Laccaria genome represents a valuable resource, the first of a series of tree community genomics projects to have passed through our production sequencing line. These community resources promise to advance a systems approach to forest genomics. - Eddy Rubin, DOE JGI Director
Rubin indicates that by using DNA sequence to survey the forest ecosystem, from the plants to symbiotic and pathogenic fungi, researchers can ultimately optimize the conditions under which a biomass plantation would thrive. The scientists now have the opportunity to gain fundamental insights into plant development and growth as related to their intimate interaction which symbiotic fungi. These insights will lead to bolstered biomass productivity and improved forests, they say.

Laccaria bicolor occurs frequently in the birch, fir, and pine forests of North America and is a common symbiont of Populus, the poplar tree whose genome was determined by the JGI in 2006 (previous post). The analysis of the 65-million-base Laccaria genome, the largest fungal genome sequenced to date, yielded 20,000 predicted protein-encoding genes, almost as many as in the human genome.

Unexpected discoveries
In sifting through these data, researchers have discovered many unexpected features, including an arsenal of small secreted proteins (SSPs), several of which are only expressed in tissues associated with symbiosis. The most prominent SSP accumulates in the extending hyphae, the tips of the fungus that colonize the roots of the host plant:
:: :: :: :: :: :: :: :: :: ::

According to Francis Martin, the Nature study's lead author, the scientists believe that the proteins specific to this host/fungus interface play a decisive role in the establishment of symbiosis. This genome exploration led Martin and his CNRS-Marseille University and DOE JGI colleagues to the unexpected observation that the genome of Laccaria lacks the enzymes involved in degradation of the carbohydrate polymers of plant cell walls but maintains the ability to degrade non-plant cell walls, which may account for Laccaria's protective capacity. These observations point towards the dual life that mycorrhizal fungi like Laccaria possess, that is, the ability to grow in soil fending off pathogens and using decaying organic matter while serving as a custodian of living plant roots.

The genome, Martin said, shows a large number of new and expanded gene families compared with other fungi. Many of these families are involved in signaling and other processes that drive the complex transition between two distinct lifestyles of Laccaria: the benign saprotroph, able to use decaying matter of animal and bacterial origins, versus the symbiont, living in mutually profitable harmony with plant roots.

The team also discovered new classes of genes that may be candidates for the complex communication that must occur between the players in the host/plant subsoil arena during fungal development. They report that fungi play a critical role in plant nutrient use efficiency by translocating nutrients and water captured in soil pores inaccessible to roots of the host plant.
The Laccaria genome sequence, its analysis, associated genomics, and bioinformatics tools provide an unprecedented opportunity to identify the key components of organism-environment interactions that modulate ecosystem responses to global change and increased nutrient input needed for faster growth. By examining and manipulating patterns of gene expression, we can identify the genetic control points that regulate plant growth and plant-mutualist response in an effort to better understand how these interactions control ecosystem function. - Francis Martin, lead author
Mycorrhizae are critical elements of the terrestrial ecosystems since approximately 85 percent of all plant species, including trees, are dependent on such interactions to thrive. Mycorrhizae significantly improve photosynthetic carbon assimilation by plants.
Host trees like Populus are able to harness this formidable web of mycorrhizal hyphae that permeates the soil and leaf litter and coax a relationship for their mutual nutritional benefit. This process is absolutely critical to the success of the interactions between the fungi and the roots of the host plant so that an equitable exchange of nutrients can be achieved. - Jerry Tuskan, co-author DOE JGI and Oak Ridge National Laboratory researcher
The DOE JGI and its collaborators have now embarked on characterizing several other poplar community symbionts that will provide a more comprehensive understanding of the biological community of the poplar forest. These include Glomus, a second plant symbiotic fungus, Melampsora, a leaf pathogen, and several plant endophytes, bacteria and fungi that live inside the poplar tree.

DOE JGI's expanding portfolio of community genomes provides the researchers with a set of resources that can be used to map out the processes by which fungi colonize wood and soil litter. These fungi interact with living plants within their ecosystem in order to perform vital functions in the carbon and nitrogen cycles that are so fundamental to sustainable plant growth.


The DOE JGI Laccaria effort was led by Igor Grigoriev. Other authors include Andrea Aerts, Erika Lindquist, Asaf Salamov, Harris Shapiro, Peter Brokstein, Chris Detter (Los Alamos National Laboratory), the DOE JGI Production Genomics Facility sequencing team led by Susan Lucas, and partners at the Stanford Human Genome Center, Jane Grimwood and Jeremy Schmutz. Projects are submitted to DOE JGI through the Community Sequencing Program.

The U.S. 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 Stanford Human Genome Center to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI's Walnut Creek, CA, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

Picture: Fruiting body of the ectomycorrhizal basidiomycete Laccaria bicolor S238N interacting with Douglas fir seedlings. Credit: INRA.

References:
F. Martin, et. al. "The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis", Nature 452, 88-92 (6 March 2008) | doi:10.1038/nature06556

DOE JGI: Laccaria bicolor project page.


Previous DOE JGI sequencing efforts include:

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



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