Nutrient availability in model wetlands helps regulate microbial metabolism and soil carbon cycling rates The Science Studying microbial communities in San Joaquin Delta rice fields, researchers linked microbial metabolism and nutrient availability to soil carbon cycling rates. The Impact Establishing the inter-relationships among microbial metabolism, nutrient availability and soil carbon cycling rates is critical to…
C. Titus Brown, University of California, Davis
How long have you collaborated with the JGI? I’m just starting my first partnership with JGI soon, but I’ve been working as part of larger JGI collaborations for about 15 years. I also worked with Jim Tiedje and Janet Jansson on the Great Prairie Grand Challenge soil sequencing project, which started about 10 years ago…
DOE User Facilities Partner for Greater Scientific Impact
EMSL and DOE JGI announce FY 2018 FICUS projects Two Department of Energy user facilities, the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI), have selected 14 proposals from a joint call for 2018 research under the Facilities Integrating Collaborations for User Science (FICUS) initiative. This was the fifth FICUS call between EMSL…
Defining Standards for Genomes from Uncultivated Microorganisms
Expanding minimum information standards for single-cell genomics, metagenomics datasets. During the Industrial Revolution, factories began relying on machines rather than people for mass production. Amidst the societal changes, standardization crept in, from ensuring nuts and bolts were made identically to maintain production quality, to a standard railroad gauge used on both sides of the Atlantic….
Tracking Microbial Succession in Petroleum Wells
Offshore subsurface reservoirs demonstrate human impacts on well microbiomes. The Science Microbes are invisible to the naked eye, but play key roles in maintaining the planet’s biogeochemical cycles. In the Earth’s subsurface, microbes have adapted to thrive in the relatively stable extreme conditions. To learn more about how some of these populations respond to disruptions…
FY2018 ETOP Call for Letters of Intent
Letters of Intent are being solicited for the Department of Energy Joint Genome Institute (DOE JGI) Emerging Technologies Opportunity Program (ETOP) 2018 award. Potential offerors must electronically submit a Letter of Intent through the DOE JGI’s proposal submission system. Letters of Intent need to be received by August 30, 2017. For examples of accepted ETOP proposals,…
Rod Wing, Arizona Genomics Institute
How long have you collaborated with the JGI? It’s probably been about ten years. We’ve been doing these high molecular weight DNA for a few projects and now through the ETOP program, we’re providing high molecular weight substrates for whole genome sequencing and for genotyping of various JGI Flagship Plant Genomes, and in support of…
Mining Eukaryotic Data for Protein Families
Despite decades of work by structural biologists, there are still ~5,200 protein families with unknown structure outside the range of comparative modeling. It has recently been shown that this gap can be largely reduced if Rosetta structure prediction pipeline is augmented with residue-residue contacts inferred from evolutionary information. Such significant boost in the number of…
Facilitating Comparative Sequence Analysis
Comparative sequence analysis, be it between genomes or metagenomes can significantly expand our biological knowledge by letting us ask questions directly of ecosystems and their inhabitants. The team proposes calculating signatures for the approximately 5,200 private microbial genomes and all of private and public metagenomes in the IMG/M database. Having the MinHash signatures will allow…
Developing Analytical Tools for Enzyme Superfamilies
A functionally diverse enzyme superfamily is a collection of enzymes that share a common ancestor and fold, as well as active site architectures and a partial reaction or other chemical capability. Putting enzymes into their superfamily context has proved to be a powerful way to understand their sequence-structure-function relationships. Metagenomic profiling of enzyme superfamilies can…