The rumen microbiome is comprised primarily of microbes such as bacteria, methanogenic archaea, fungi, ciliate protozoa and viruses that have evolved to act together to rapidly breakdown of complex plant sugars, and ferment the released sugars to produce short-chain fatty acids. Methane is a potent greenhouse gas (GHG) with a global warming potential 25 times…
Fungal enzymes in the cow rumen
The genes and genomes of microbes in the cow rumen represent a valuable source for new biomass-degrading enzymes that might enable processes to more efficiently convert biomass into biofuels. Fungi make up less than 10 percent of the microbial biomass in the rumen and fungal enzymes appear to have higher specific activities towards plant cell…
Founding a grass transcription factor library
Sequenced at the DOE JGI, Brachypodium distachyon is a small temperate grass that is being used as a model for potential energy crops such as switchgrass, sorghum, and Miscanthus. One of the goals in cultivating bioenergy crops is producing enough biomass to convert and use for biofuel production to meet the nation’s needs. This project…
Focusing on the Agave microbiome
Deserts and drylands currently encompass 40 percent of the Earth’s land surface and a further increase in such areas due to climate change and other processes is expected. There are approximately 200 species of Agave, most native to deserts and drylands in central Mexico and the Southwestern United States. Recently identified as candidate bioenergy feedstocks,…
Macondo wellhead metagenomes
The 2010 Deepwater Horizon oil spill presented researchers with an opportunity to employ a variety of approaches to quantify and model the microbial community composition and activity through successive metabolic petroleum hydrocarbon degradation. The Macondo wellhead oil leak, in the Gulf of Mexico, released a complex mixture of hydrocarbons into the water column that stimulated…
Extremophilic microbial mat communities
Found worldwide, microbial mat communities are often the pioneering species in perturbed environments and can represent the only biota in extreme habitats. These associations are well-adapted to a range of harsh conditions that include extremes of temperature, salinity, high or low oxygen levels, and nutrient deprivation. In many cases, microbial mats are highly productive biochemical…
NutNet soil metagenomes
Terrestrial ecosystems worldwide are receiving elevated inputs of nitrogen and recent studies suggest that the additional nitrogen is impacting soil carbon sequestration rates. It has been speculated that nitrogen additions alter the microbial processing of organic carbon pools, inhibiting decomposition of certain pools and accelerating soil carbon sequestration. This project focuses on shotgun metagenomic sequencing…
Single-cell sequencing of iron-oxidizing bacteria
Iron is the fourth most abundant element in the Earth’s crust and is potentially one of the most abundant energy sources on Earth. Deep sea hydrothermal vents deposit iron oxides into the oceans annually. Several decades ago, the first hints of unusual microbial communities associated with iron oxides at seamounts came from samples collected by…
Bacterial symbionts of gutless marine worms
More than 100 species of gutless worms have been found in marine sediments around the world, and they have formed symbiotic relationships with bacteria that provide them with nutrition and have enabled them to colonize nutrient-poor environments. The symbionts are so efficient at feeding their hosts and recycling their waste compounds that the worms have…
Carbon-storing bacteria in rhizosphere soils
Microbes are able to store carbon under suboptimal growth conditions in culture, but the extent to which they store carbon in bulk or rhizosphere soil are not well understood. One stress response observed in microbes is the production of carbon storage granules as a means of trapping the needed carbon in the soil. Understanding the…