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    Mongabay, a leading resource for news and perspectives on environmental and conservation issues related to the tropics, has launched Tropical Conservation Science - a new, open access academic e-journal. It will cover a wide variety of scientific and social studies on tropical ecosystems, their biodiversity and the threats posed to them. Tropical Conservation Science - March 8, 2008.

    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.

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Monday, June 09, 2008

Argonne - UChicago joint venture bolsters genomic sequencing capabilities; focus on microbial soil carbon sequestration

More and more scientists are urging us to manage carbon emissions radically to avoid dangerous ecological tipping points. This means we have to look at techniques to actively remove CO2 from the atmosphere, instead of merely avoiding new emissions. According to NASA's Jim Hansen, humanity's target should be a reduction of atmospheric CO2 levels to 350ppm (from current levels of 387ppm).

There are many potential carbon sequestration techniques which can do the trick, ranging from risky or energy inefficient geo-engineering methods such as iron seeding oceans or building 'synthetic trees' which trap CO2 from the air, to more practical options such as capturing and storing CO2 from biomass power plants.

The most natural and cost-effective way to sequester carbon is by growing trees, and via biochar. The biochar concept, also known as agrichar or 'terra preta', consists of carbonizing renewable biomass to sequester it into soils where the recalcitrant C can stay locked up for centuries and possibly millennia (more here). Biochar production yields renewable energy and makes problem soils more fertile, allowing for even more biomass to grow and to scrub more CO2 out of the atmosphere.

Because of this interesting synergy, biochar and soil carbon sequestration is receiving more and more attention from climate scientists (Hansen sees it as one of the four key concepts we must implement to achieve the 350ppm target). But many of the precise effects of char on soil microbial communities remains to be researched. Field and lab trials with different soils have already shown that biochar boosts soil microbial activity, crucial for providing nutrients to plants. Other researchers have found biochar to reduce two very potent greenhouse gases that escape from soils, namely nitrous oxide and methane. Microbes too are responsible for managing the emergence of these climate destructive gases.

Given these important functions and encouraging results, scientists want to zoom in further on the rich diversity of soil bateria and their potential role in mitigating climate change. The soil is a universe teeming with life, containing unknown numbers of different species of microorganisms, most of them never studied. Soils contain more carbon than all vegetation and the atmosphere combined, and microbes are the managers of this material.

So how to study these key organisms? Efficient genome sequencing would be a first crucial step. This is precisely what the Institute for Genomics and Systems Biology (IGSB) wants to do. The IGSB, a joint venture of the U.S. Department of Energy's (DOE) Argonne National Laboratory and the University of Chicago, today announced it has acquired two new instruments that provide an enhanced ability to sequence genomes more quickly and broadly.

The 454 FLEX is ideally suited for studying microbial communities by de novo sequencing. It provides 400,000 DNA fragments of about 250 base pairs each - or 100 million base pairs per run - that represent either a significant part of the genome of a single organism or a random snapshot of parts of multiple genomes.
It used to be that only species that could be cultivated, or grown in pure culture, could be sequenced. The capabilities of the new Roche 454 FLEX and Illumina Solexa Genome Sequencer now allow scientists that use the machines to skip the cultivation step. Eliminating that step will save time and speed up the research process, while maintaining accurate sequencing results. - Kevin White, IGSB director
The other machine, a Solexa Genome Sequencer, is targeted at resequencing. Compared to the Roche 454 FLEX, it generates more but shorter reads, creating 40 million reads with a current read length of 18 to 36 base pairs - or about 1 billion base pairs per run - depending on the application.

The machines were purchased to facilitate research for three Argonne Laboratory-Directed Research and Development projects dealing with soil microbes. The first project is led by Michael Miller, a terrestrial ecologist, and Folker Meyer, a computational biologist in IGSB. It will use the genome sequencing to enhance our understanding of soil CO2 sequestration capability on the microbial level:
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In another project, Argonne's soil ecology group is using metagenome sequencing to study the microbial population in chronoseries plots at DOE's Fermi National Accelerator Laboratory.

In a third project, Argonne's environmental remediation program is studying the role played by microbial communities in subsurface remediation of inorganic contaminates using metagenome sequencing.

IGSB's sequencing group plays an active role in the design and optimization of experiments using DNA sequencing technology, such as developing and optimizing protocols for DNA isolation from environment as diverse as subsurface soil and plant leaves. The group also works with researchers to develop protocols for DNA extraction and to conduct downstream bioinformatics analyses.

The new machines are also open to other Argonne and University of Chicago researchers who need genetic samples sequenced. In the near future, the sequencing instruments will be available to select peer-reviewed proposals from researchers from other organizations.

Argonne's genomics research is primarily funded DOE's Office of Science, which supports research that provides a fundamental scientific understanding of plants and microbes necessary to develop strategies for sequestering carbon gases, producing biofuels and cleaning up waste.

Argonne National Laboratory brings the world's brightest scientists and engineers together to find exciting and creative new solutions to pressing national problems in science and technology. The United States' first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America 's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science.

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