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(More) Genomics of Energy and Environment

The world's waters are teeming with microorganisms, but what, exactly, are they all? What do they do?

Moreover, as the Bigelow Laboratory for Ocean Sciences' Ramunas Stepanauskas considered at the US Department of Energy Joint Genome Institute's 7th annual User Meeting, "what if every cell is different?"

During his talk, Stepanauskas discussed how researchers are applying single-cell sequencing techniques to address fundamental questions like "what is a microbial species?" and "do uncultured microbes differ from their cultured relatives?" He also spoke about the Bigelow Laboratory's Single Cell Genomics Center, which was launched as a fee-for-service sequencing center in 2009 and currently has more than 300,000 single cells in its pipeline. Single cell genomics, Stepanauskas said, could help researchers resolve genome recovery "from the 'uncultured majority.'"

Oregon State University's Stephen Giovannoni then outlined the potential causes and consequences of genome size in SAR11 marine bacteria. "The small genome of SAR11 appears to be an extreme case of streamlining selection," Giovannoni told User Meeting attendees, later adding the content of the SAR11 genome is highly conserved across large evolutionary distances.

The University of Arizona's Matthew Sullivan spoke about his group's efforts toward characterizing "the global ocean virome." Thus far, the team has examined 32 Pacific Ocean viral metagenomes. Sullivan also talked about using protein cluster data to define the "core" and "flexible" ocean virome.

Later, Richard Sayre at the Los Alamos National Laboratory discussed his work on optimizing biomass production in transgenic microalgae. Sayre said that developing "transgenic algae that self-regulate antennae size depending on light intensity," as his group aims to do, could have implications "for improving photosynthetic efficiency in bioenergy crops."

Finally, Wellington Muchero at the Oak Ridge National Laboratory emphasized the importance of searching for variation within intergenic regions during his talk on the genetics of glucose release phenotype in Populus [trichocarpa], or poplar. Muchero and his team genotyped more than 1,000 Populus samples collected at sites between Sacramento, Calif., and British Columbia. In his talk, Muchero outlined the multiple eQTL- and association-mapping approaches his team took to zero in on 13 trait-assocated SNPs within the same gene — an MYB transcription factor. Of those 13 SNPs, Muchero and his colleagues found two showed the highest association with both glucose and glucose/xylose release, he said.

For more JGI User Meeting coverage, Jonathan Eisen has created a Storify, cataloging tweets, images, and blog posts from the Walnut Creek gathering.

The Scan

CDC Calls Delta "Variant of Concern"

CNN reports the US Centers for Disease Control and Prevention now considers the Delta variant of SARS-CoV-2 to be a "variant of concern."

From FDA to Venture Capital

Former FDA Commissioner Stephen Hahn is taking a position at a venture capital firm, leading some ethicists to raise eyebrows, according to the Washington Post.

Consent Questions

Nature News writes that there are questions whether informed consent was obtained for some submissions to a database of Y-chromosome profiles.

Cell Studies on Multimodal Single-Cell Analysis, Coronaviruses in Bats, Urban Microbiomes

In Cell this week: approach to analyze multimodal single-cell genomic data, analysis of bat coronaviruses, and more.