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Green foxtail as a model C4 grass

Setaria viridis is the wild progenitor of S. italica, more commonly known as foxtail millet. Green foxtail is related to other grasses that have been considered candidate bioenergy feedstocks such switchgrass, Miscanthus and sorghum. Both green foxtail and foxtail millet have been sequenced by the DOE JGI, and this project focuses on understanding and promoting… [Read More]

Mediterranean Grassland Soil Metagenome

Mediterranean ecosystems and grasslands are considered among the most vulnerable to biodiversity loss due to global environmental change. For the Mediterranean grasslands of California, climate models have predicted decreasing precipitation combined with elevated temperatures. The result could lead to accelerated decomposition and mineralization of soil organic matter in the rhizosphere, that area where the soil… [Read More]

Metagenomic IFRC study for bioremediation

The Department of Energy Integrated Field Research Challenge (IFRC) site at Rifle, Colorado is a widely-used bioremediation research site. Using the resident microbes to help bioremediate an area is an important, potentially cost-effective environmental cleanup strategy. This project involves the application of massive sequencing to several subsurface samples to be collected from across the (unstimulated)… [Read More]

Understanding a lichen microecosystem

Lobaria pulmonaria is a lichen found in the northern hemisphere that contributes locally to carbon cycling at an ecosystem level. Lichens themselves are microecosystems composed of fungi, unicellular green algae and cyanobacteria while also hosting other organisms. These associations involve coordinating and reshaping the growth of very different species – from two – sometimes three… [Read More]

“Deep MalaspinOmics” and the Dark Ocean

Located 200 meters underwater, the dark ocean does not receive enough light to support photosynthesis. In the oceans, the photosynthesis takes place in the top layer where the sunlight penetrates. Microbes that live in deeper waters known informally as the “twilight zone” use a significant portion of the carbon produced in the waters where photosynthesis… [Read More]

Algae and the Carbon Cycle in the North Sea

Marine algae conduct about half of the global carbon dioxide fixation, impacting organic net primary production. The role of bacteria in this process is as yet only poorly understood but of interest to a broad scientific community. The COGITO (Coastal Microbe Genomic & Taxonomic Observatory) project is an integrative marine microbiology ecosystems study that is… [Read More]

Single-cell genomics of subsurface microbes

The deep subsurface biome is dominated by unicellular microbes and comprises a major fraction of the global living carbon mass on Earth. Results from studies conducted over the past 20 years suggest that the deep subsurface biosphere differs from the surface photosphere, resulting in the perception that subsurface microbes have the streamlined genomes of specialists… [Read More]

DOE JGI Plant Flagship Gene Atlas

The DOE JGI sequenced the model alga C. reinhardtii, soybean (G. max), the moss P. patens, the poplar tree (P. trichocarpa), and foxtail millet (Setaria italica) to create a platform for DOE plant science research. These plants are among those that have been designated as DOE JGI Plant Flagship Genomes. As part of the Flagship… [Read More]

Protein Modeling for Biofuel Production and Carbon Cycle Studies

Novel strategies are needed in order to resolve the challenges we currently face in energy production and global carbon cycling. On the forefront of possible routes to address these challenges is the application of biotechnology to engineer systems for the production of fuels, materials, and the conversion of carbon dioxide into high value products. Current… [Read More]

Plant-bacteria symbiosis for nitrogen fixation

Plants in the legume family form symbioses with nitrogen-fixing soil bacteria or rhizobia that provide a sustainable nitrogen source to improve soil fertility in agricultural settings. Symbiotic nitrogen fixation is central to any plan for energy-sustainable production of food or fuel. Crop plants for food, oil, and green manure are able to produce high-protein seeds… [Read More]