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Insights on tree-subsurface microbial interactions

In forested watersheds, trees are center stage in the carbon cycle. However, tree-based photosynthetic carbon fixation is modulated by interactions with the subsurface microbial biosphere. Previous studies focused on the root rhizosphere, but recent work at the Eel River Critical Zone Observatory (CZO) in Northern California suggests much of the carbon, water and nutrient exchange… [Read More]

An ENCODE-like model for Chlamy

The objective of this project is to to perform a comprehensive study of regulatory (transcriptional and miRNA) networks underlying the nutrient stress-induced lipid accumulation response. They intend to use the information to develop an ENCODE-like working model of DNA regulatory elements associated with nutrient-responsive control of lipid accumulation phenotype (LAP) and biomass production in Chlamydomonas… [Read More]

Banfield collaboration in Quanta magazine

“We used to think there were just plants and animals,” said Edward Rubin, director of the U.S. Department of Energy’s Joint Genome Institute. “Then we got microscopes, and got microbes. Then we got small levels of DNA sequencing.” Quanta magazine focused on a recent project led by Jill Banfield in Colorado, one that significantly increased the known… [Read More]

Cleaning Up Bunker Oil with White Rot Fungi

Researchers evaluate how fungi better known for breaking down plant biomass do in a bioremediation application. The Science: Researchers evaluated the potential capabilities of six white rot fungi to break down oil in contaminated canal waters. The Impact: Though white rot fungi are known for their capabilities in breaking down components of plant cell walls,… [Read More]

Unearthing Cornerstones in Root Microbiomes

Defining core members of a microbial community for normal plant growth Like the tip of an iceberg, a plant sprouting from the soil barely hints at what lies beneath. At the nexus where roots and soil intersect are thriving microbial communities that play important roles in plant health and growth. Understanding how plant yields can… [Read More]

The MiSIng Piece Revealed: Classifying microbial species in the genomics era

The rapid explosion in the throughput of DNA sequencing due to new technology platforms is fueling an increase in the number of sequenced microbial genomes and driving much greater availability of these data to the research community. Traditionally, identifying the microorganisms selected for sequencing is often decided on the basis of a single universal marker… [Read More]

Celebrating the Eucalyptus Reference Genome

New Phytologist dedicates an entire issue to various research directions based on the tree genome. The Science: Building off the Eucalyptus grandis tree genome that researchers at the DOE Joint Genome Institute helped sequence and analyze, several researchers demonstrate the utility of the reference genome in the June 2015 special issue of New Phytologist. The… [Read More]

Confirming Microbial Lineages Through Cultivation-Independent Means

Collaborative work culminates in evidence of a single candidate bacterial phylum. The number of microbes found on Earth has been compared to the number of stars in the Milky Way. Yet the proportion of those microbes that can actually be grown under laboratory conditions is so small it would be akin to those stars that… [Read More]

Collaborator Janet Jansson in Quanta magazine

“[S]oon after the turn of the century, new high-octane DNA sequencing methods made it possible to sequence thousands or even millions of genes almost instantly. These new, speedier methods meant researchers could easily sequence the collective genomes of the sample, known as a metagenome, for the first time. Suddenly, it was possible to scan the… [Read More]