Microbial sRNAs are untranslated short transcripts that generally reside within intergenic regions on microbial genomes. Most microbial sRNAs function as regulators, and many are currently known to be involved in environmentally significant processes including amino acid and vitamin biosynthesis, quorum sensing, and photosynthesis. Using publicly available metatranscriptomes and metagenomes, as well as metagenomes and metatranscriptomes…
A Scalable Process for Charting Biogeochemical Cycles
Microbial communities drive matter and energy transformations through distributed networks of metabolite exchange that can be reprogrammed though viral infection. In this light, individual microorganisms function as information processing units implementing a distributed genetic algorithm manifested in biologically driven redox reactions on a planetary scale. A core set of genes that evolved early in the…
Population Studies of Soil Microbial Communities
How microbial communities contrast with respect to taxonomic and functional composition within and between soil ecosystems remains an unresolved question that is central to modeling soil functioning and services. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared…
DOE User Facilities Join Forces to Tackle Biology’s Big Data
Inaugural Collaborative Science Call Yields Six Proposals Melding Genomics, Supercomputing Six proposals have been selected to participate in a new partnership between two U.S. Department of Energy (DOE) user facilities through the “Facilities Integrating Collaborations for User Science” (FICUS) initiative. The expertise and capabilities available at the DOE Joint Genome Institute (JGI) and the National…
Insights into A Eukaryotic Alga
The genome of Porphyra umbilicalis reveals the mechanisms by which it thrives in the intertidal zone The Science Through the Community Science Program of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, a 50-member team led by University of Maine, Carnegie Institution for Science, and East…
New Technology to Access Microbial Dark Matter
Demonstrating the microfluidic-based, mini-metagenomics approach on Yellowstone hot springs samples. The Science Stanford researchers extracted 29 novel microbial genomes from Yellowstone hot spring samples while still preserving single-cell resolution to enable accurate analysis of genome function and abundance. The work was enabled by the Emerging Technologies Opportunity Program (ETOP) of the U.S. Department of Energy…
Tiny Green Algae Reveal Large Genomic Variation
First complete picture of standing genetic variation within a natural population. The Science Ostreococcus are tiny green algae that are the bases of many marine food webs. A decade after the complete representative genomes of three Ostreococcus picoplankton groups were sequenced, researchers have sequenced and analyzed the genomes of 13 members of a natural Ostreococcus…
Mutant Rice Database for Bioenergy Research
Genome-wide rice studies yield first major, large-scale collection of mutations for grass models. The Science Fast-neutron irradiation, exposure to high energy neutrons, induces a wide variety of mutations by making changes in DNA. Using this approach, rice researchers were able to create the first major, large-scale collection of mutations for grass models. Resequencing the 1,504…
Lessons from Simulating A Deep Ocean Oil Spill
Metagenome pipeline helps researchers resolve near-complete microbial genomes involved in Deepwater Horizon oil spill. The Science The 2010 Deepwater Horizon oil spill released 4.1 million barrels of oil into the Gulf of Mexico and was the first major release of oil and natural gases into the deep ocean (1,500 meters). Due to the depth of…
Uncovered: 1000 New Microbial Genomes
Potential biotech applications seen with release of 1,003 reference bacterial and archaeal genomes. The number of microbes in a handful of soil exceeds the number of stars in the Milky Way galaxy, but researchers know less about what’s on Earth because they have only recently had the tools to deeply explore what is just…