Biosciences Area

JGI Overhauls Perception of Inovirus Diversity

Inoviruses are filamentous viruses with small, single-stranded DNA genomes and a unique chronic infection cycle. In Nature Microbiology, a team led by DOE Joint Genome Institute (JGI) researchers applied machine learning to publicly available microbial genomes and metagenomes to search for inoviruses. The search tool combed through more than 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously known inovirus genomes. The results revealed inoviruses are in every major microbial habitat—including soil, water, and humans—around the world.

“We’re not sure why we systematically manage to miss them; maybe it’s due to the way we currently isolate and extract viruses,” said the study’s lead author Simon Roux, a JGI research scientist in the Environmental Genomics group. Click here to read the full story on the JGI site.

JGI Helps Determine Archaeal Symbiotic Lifestyles

Symbiotic relationships are long-term biological interactions between one or more biological organisms. Nanohaloarchaea are part of the DPANN superphylum of extremophilic archaea first outlined by JGI scientists and their collaborators in 2013. While most DPANN lineages are predicted symbionts, the Nanohaloarchaeota were predicted to be capable of autonomous growth because they had larger genome sizes and their cells were not observed to associate with host cells.

In the Proceedings of the National Academy of Sciences, a team led by Rick Cavicchioli at the University of New South Wales along with researchers at the Joint Genome Institute (JGI) experimentally demonstrated that Nanohaloarchaeota are not free-living archaea but rather symbionts. Click here to read the JGI science highlight.

JGI Researchers Featured in mSystems Special Issue

Three Joint Genome Institute researchers are among the authors who offered perspectives on what the next five years of innovation could look like for a special issue of the journal mSystems. In one article, Micro-Scale Applications head Rex Malmstrom and Metagenome Program head Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental sample. In a separate article, research scientist Simon Roux, a member of Eloe-Fadrosh’s Environmental Genomics group, makes a pitch for readers to get involved in the developing field of virus ecogenomics.

Read more from JGI.

Biosciences Area FY19 LDRD Projects

The projects of 13 Biosciences Area scientists and engineers received funding through the FY19 Laboratory Directed Research and Development (LDRD) program. The funded projects span a diverse array of topics and approaches including the harnessing of microbiome data to uncover patterns of mutualism, evaluating radiobiological effects of laser-accelerated ion beams, improving bioenergy yield under drought stress, and the application of machine learning in tomogram segmentation. Lab-wide, 89 projects were selected from a field of 158 proposals. Biosciences Area efforts account for 15.07 percent of the $22.2 million allocated.

Biosciences Area FY18 LDRD Projects

The projects of 13 Biosciences Area scientists and engineers received funding through the FY18 Laboratory Directed Research and Development (LDRD) program. These projects span a diverse array of topics and approaches including the study of microbiomes in relation to patterns of mutualism, crop productivity, and gut health; synthetic biology for engineering biosurfactant production and energy conversion pathways; and the application of technologies such as machine learning, high-resolution optical microscopy, and single-cell transcriptomics. Together, these efforts account for 18.75 percent of the $20 million allocated. Lab-wide, 74 projects were selected from a field of 215.

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