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    Note: Biopact's mail-server is being changed, so any incoming mails will bounce-back. The problem will be solved in the coming 12-24 hours. Biopact Team - November 22, 2007.

    Analysts think Vancouver-based Ballard Power Systems, which pumped hundreds of millions and decades of research into developing hydrogen fuel cells for cars, is going to sell its automotive division. Experts describe the development as "the death of the hydrogen highway". The problems with H2 fuel cell cars are manifold: hydrogen is a mere energy carrier and its production requires a primary energy input; production is expensive, as would be storage and distribution; finally, scaling fuel cells and storage tanks down to fit in cars remains a huge challenge. Meanwhile, critics have said that the primary energy for hydrogen can better be used for electricity and electric vehicles. On a well-to-wheel basis, the cleanest and most efficient way to produce hydrogen is via biomass, so the news is a set-back for the biohydrogen community. But then again, biomass can be used more efficiently as electricity for battery cars. Canada.com - November 21, 2007.

    South Korea plans to invest 20 billion won (€14.8/$21.8 million) by 2010 on securing technologies to develop synthetic fuels from biomass, coal and natural gas, as well as biobutanol. 29 private companies, research institutes and universities will join this first stage of the "next-generation clean energy development project" led by South Korea's Ministry of Commerce, Industry and Energy. Korea Times - November 19, 2007.

    OPEC leaders began a summit today with Venezuelan President Hugo Chavez issuing a chilling warning that crude prices could double to US$200 from their already-record level if the United States attacked Iran or Venezuela. He urged assembled leaders from the OPEC, meeting for only the third time in the cartel's 47-year history, to club together for geopolitical reasons. But the cartel is split between an 'anti-US' block including Venezuela, Iran, and soon to return ex-member Ecuador, and a 'neutral' group comprising most Gulf States. France24 - November 17, 2007.

    The article "Biofuels: What a Biopact between North and South could achieve" published in the scientific journal Energy Policy (Volume 35, Issue 7, 1 July 2007, Pages 3550-3570) ranks number 1 in the 'Top 25 hottest articles'. The article was written by professor John A. Mathews, Macquarie University (Sydney, Autralia), and presents a case for a win-win bioenergy relationship between the industrialised and the developing world. Mathews holds the Chair of Strategic Management at the university, and is a leading expert in the analysis of the evolution and emergence of disruptive technologies and their global strategic management. ScienceDirect - November 16, 2007.

    Timber products company China Grand Forestry Resources Group announced that it would acquire Yunnan Shenyu New Energy, a biofuels research group, for €560/$822 million. Yunnan Shenyu New Energy has developed an entire industrial biofuel production chain, from a fully active energy crop seedling nursery to a biorefinery. Cleantech - November 16, 2007.

    Northern European countries launch the Nordic Bioenergy Project - "Opportunities and consequences of an expanding bio energy market in the Nordic countries" - with the aim to help coordinate bioenergy activities in the Nordic countries and improve the visibility of existing and future Nordic solutions in the complex field of bioenergy, energy security, competing uses of resources and land, regional development and environmental impacts. A wealth of data, analyses and cases will be presented on a new website - Nordic Energy - along with announcements of workshops during the duration of project. Nordic Energy - November 14, 2007.

    Global Partners has announced that it is planning to increase its refined products and biofuels storage capacity in Providence, Rhode Island by 474,000 barrels. The partnership has entered into agreements with New England Petroleum Terminal, at a deepwater marine terminal located at the Port of Providence. PRInside - November 14, 2007.

    The Intergovernmental Panel on Climate Change (IPCC) kicks off the meeting in Valencia, Spain, which will result in the production of the Synthesis Report on climate change. The report will summarize the core findings of the three volumes published earlier by the separate working groups. IPCC - November 12, 2007.

    Biopact's Laurens Rademakers is interviewed by Mongabay on the risks of large-scale bioenergy with carbon storage (BECS) proposals. Even though Biopact remains positive about BECS, because it offers one of the few safe systems to mitigate climate change in a drastic way, care must be take to avoid negative impacts on tropical forests. Mongabay - November 10, 2007.

    According to the latest annual ranking produced by The Scientist, Belgium is the world's best country for academic research, followed by the U.S. and Canada. Belgium's top position is especially relevant for plant, biology, biotechnology and bioenergy research, as these are amongst the science fields on which it scores best. The Scientist - November 8, 2007.

    Mascoma Corporation, a cellulosic ethanol company, today announced the acquisition of Celsys BioFuels, Inc. Celsys BioFuels was formed in 2006 to commercialize cellulosic ethanol production technology developed in the Laboratory of Renewable Resources Engineering at Purdue University. The Celsys technology is based on proprietary pretreatment processes for multiple biomass feedstocks, including corn fiber and distiller grains. The technology was developed by Dr. Michael Ladisch, an internationally known leader in the field of renewable fuels and cellulosic biofuels. He will be taking a two-year leave of absence from Purdue University to join Mascoma as the company’s Chief Technology Officer. Business Wire - November 7, 2007.

    Bemis Company, Inc. announced today that it will partner with Plantic Technologies Limited, an Australian company specializing in starch-based biopolymers, to develop and sell renewably resourced flexible films using patented Plantic technology. Bemis - November 7, 2007.

    Hungary's Kalocsa Hõerõmû Kft is to build a HUF 40 billion (€158.2 million) straw-fired biomass power plant with a maximum capacity of 49.9 megawatts near Kalocsa in southern Hungary. Portfolio Hungary - November 7, 2007.

    Canada's Gemini Corporation has received approval to proceed into the detailed engineering, fabrication and construction phases of a biogas cogeneration facility located in the Lethbridge, Alberta area, the first of its kind whereby biogas production is enhanced through the use of Thermal Hydrolysis technology, a high temperature, high pressure process for the safe destruction of SRM material from the beef industry. The technology enables a facility to redirect waste material, previously shipped to landfills, into a valuable feedstock for the generation of electricity and thermal energy. This eliminates the release of methane into the environment and the resultant solids are approved for use as a land amendment rather than re-entering the waste stream. In addition, it enhances the biogas production process by more than 25%. Market Wire - November 7, 2007.

    A new Agency to manage Britain's commitment to biofuels was established today by Transport Secretary Ruth Kelly. The Renewable Fuels Agency will be responsible for the day to day running of the Renewable Transport Fuels Obligation, coming into force in April next year. By 2010, the Obligation will mean that 5% of all the fuels sold in the UK should come from biofuels, which could save 2.6m to 3m tonnes of carbon dioxide a year. eGov Monitor - November 5, 2007.

    Prices for prompt loading South African coal cargoes reached a new record last week with a trade at $85.00 a tonne free-on-board (FOB) for a February cargo. Strong Indian demand and tight supply has pushed South African prices up to record levels from around $47.00 at the beginning of the year. European DES/CIF ARA coal prices have remained fairly stable over the past few days, having traded up to a record $130.00 a tonne DES ARA late last week. Fair value is probably just below $130.00 a tonne, traders said. At this price, some forms of biomass become directly competitive with coal. Reuters Africa - November 4, 2007.

    The government of India's Harayana state has decided to promote biomass power projects based on gasification in a move to help rural communities replace costly diesel and furnace oil. The news was announced during a meeting of the Haryana Renewable Energy Development Agency (HAREDA). Six pilot plants have demonstrated the efficiency and practicability of small-scale biomass gasification. Capital subsidies will now be made available to similar projects at the rate of Rs 2.5 lakh (€4400) per 100 KW for electrical applications and Rs 2 lakh (€3500) per 300 KW for thermal applications. New Kerala - November 1, 2007.

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Thursday, November 22, 2007

Scientists sequence and analyse genomes of termite gut microbes to yield novel enzymes for cellulosic biofuel production

An international team of scientists has sequenced and analysed the genomes of the microbes found in termite guts. Termites - notorious for their voracious appetite for wood, rendering houses to dust - may provide the biochemical means to a greener biofuel future. Termite guts harbor a gold mine of microbes that have now been tapped as a rich source of enzymes for improving the conversion of abundant biomass and wood to valuable next-generation biofuels. The research has long been anticipated by the bioenergy community.

The sequencing was conducted by the U.S. Department of Energy Joint Genome Institute (DOE JGI), which leads sequencing of energy crops and microorganisms for bioenergy (more here), the California Institute of Technology, Verenium Corporation (formerly Diversa), a biofuels company, INBio, the National Biodiversity Institute of Costa Rica, and the IBM Thomas J. Watson Research Center. The analysis is highlighted in the November 22 edition of the journal Nature.

The termite is a remarkable machine. It can digest a frightening amount of wood in a very short time, as anyone who has had termites in their house is painfully aware. Instead of using harsh chemicals or excess heat to do so, termites employ an array of specialized microbes in their hindguts to break down the cell walls of plant material and catalyze the digestion process.

Industrial-scale DNA sequencing by DOE JGI was key to identifying the genetic structures that comprise the tools that termites use. The task now is to discover the metabolic pathways generated by these structures to figure out how nature digests plant materials. Scientists can then synthesize the novel enzymes discovered through this project to accelerate the delivery of the next generation of cellulosic biofuels.

While termites have been the subject of keen scientific study for more than a century, the precise identity and role of the microbes from their digestive tract remained a mystery. With this new work, the symbiotic orchestration of these compartmentalized, complex microbial communities required for wood digestion is now coming to light.

Like cows, termites have a series of stomachs, each harboring a distinct community of microbes under precisely defined conditions. These bugs within bugs are tasked with particular steps along the conversion pathway of woody polymers to sugars that can then be fermented into fuels such as ethanol. The mandibles of the insect chomp the wood into bits, but the real work is conducted in the dark recesses of the belly, where the enzymatic juices exuded by microbes attack and deconstruct the cellulose and hemicellulose, which, along with lignin, are the basic building blocks of wood.

The tiny insects that gave up their stomach contents to advance the frontiers of science were isolated on a safari into the rainforest of Costa Rica, the world's geographic hotbed of biodiversity for termites, by co-author Jared Leadbetter of Cal Tech, first author Falk Warnecke of DOE JGI's Microbial Ecology Program, and members of Verenium and INBio. Traipsing through the jungle, the team came upon a massive, tumor-like nest of termites clinging to an otherwise nondescript tree. With a flick of a machete, the contents of this dense network of tunnels forged from wood waste were revealed, along with a frenzy of higher termites from the genus Nasutitermes (picture), which are only about the size of the date imprinted on a penny:
:: :: :: :: :: :: :: :: :: :: :: ::

Foregoing the funnel-headed "soldiers," the project focused on the larger "workers," with bulbous heads and inflated bellies. In the laboratory of INBio, researchers armed with fine forceps and needles painstakingly extracted the contents of the workers' third paunch or hindgut, referred to as P3, a distended kink in the convoluted plumbing system of the termite. Each sample was barely visible to the naked eye, and care was taken not to contaminate it with material from neighboring stomachs. Contents from 165 specimens were purified, yielding only a few valuable drops - a veritable microbial mosh pit - that was sent on ice to Verenium for DNA extraction and preparation, then on to DOE JGI's Walnut Creek (CA) Production Genomics Facility for sequencing.

From the sample, about 71 million letters of fragmented genetic code were elaborated and computationally reassembled, like putting Humpty Dumpty back together again, to tease out the identities of the microbial players in the mixture and the metabolic profile of the enzymes that they produce. From this reconstructed liquid puzzle emerged the identities of a dozen different phyla - broad groupings of microbial life forms.
Our analysis revealed that the hindgut is dominated by two major bacterial lineages, treponemes and fibrobacters. Treponemes have long been recognized in the termite gut due to their distinctive cork-screw shape, but fibrobacters were an exciting new find, because they have relatives in the cow rumen known to degrade cellulose. We could directly link the termite fibrobacters and treponemes to enzymes capable of breaking down wood. However, fibrobacters are specialists in this regard and don't appear to participate in sugar fermentation, leaving that to the treponemes. This project has really given me a new appreciation for the lowly termite, a mobile miniature bioreactor. - Phil Hugenholtz, DOE JGI's Microbial Ecology Program head, co-author
In the termite P3 compartment alone, more than 500 genes related to the enzymatic deconstruction of cellulose and hemicellulose were identified by Hugenholtz and colleagues. This dataset has since been uploaded by DOE JGI onto its metagenome data management and analysis system, IMG/M for public access and further analysis.
Adapting these findings for an industrial-scale system is far from easy. Termites can efficiently convert milligrams of lignocellulose into fermentable sugars in their tiny bioreactor hindguts. Scaling up this process so that biomass factories can produce biofuels more efficiently and economically is another story. To get there, we must define the set of genes with key functional attributes for the breakdown of cellulose, and this study represents an essential step along that path. - Eddy Rubin, JGI Director
Nature paper first author Falk Warnecke is a postdoctoral fellow in the Hugenholtz lab. Other DOE JGI authors include Natalia Ivanova, Rotem Sorek, Susannah Tringe, Hector Garcia Martin, Victor Kunin, Daniel Dalevi, Julita Madejska, Edward Kirton, Darren Platt, Ernest Szeto, Asaf Salamov, Kerrie Barry, Natalia Mikhailova, Nikos Kyrpides, and Director Rubin.

These findings follow on the heels of the announcement by DOE Secretary Samuel Bodman in June that DOE will invest up to $375 million in three new Bioenergy Research Centers to accelerate basic research in the development of cellulosic ethanol and other biofuels. DOE JGI will conduct genome sequencing in support of these centers (earlier post).

The termite hindgut whodunit builds upon DOE JGI's pioneering "metagenomic" research, where genetic material is isolated, identified, and characterized directly from environmental samples, providing a profile of a particular (often extreme) ecological niche. Published investigations by DOE JGI include glimpses into such diverse slices of the biosphere as acid mine drainage, a gutless worm, farm soil, submerged whalebones, and sewage sludge.

Currently among the scores of projects in the sequencing queue at DOE JGI are metagenomes from contents of the Tammar wallaby forestomach, the Asian longhorned beetle gut, and other exotic species that promise to be treasure troves of enzymes involved in cellulose deconstruction. These targets were submitted through DOE JGI's Community Sequencing Program (CSP), which provides the scientific community with access to high-throughput sequencing for projects of relevance to DOE missions.

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: Nasutitermes corniger termites photographed in Puerto Rico. Credit: David Gilbert, DOE Joint Genome Institute.

Falk Warnecke, et al., "Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite", Nature 450, 560-565 (22 November 2007) | doi:10.1038/nature06269

Andreas Brune, "Microbiology: Woodworker's digest", Nature 450, 487-488 (22 November 2007) | doi:10.1038/450487a; Published online 21 November 2007

Biopact: U.S. Dept. of Energy to invest $375 million in 3 Bioenergy Research Centers - June 27, 2007

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

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


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