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A History of Phage-Host Interactions With Help From CRISPRs

A tool to help microbial ecologists link phages to hosts in ecological studies. The Science: Using metagenomic datasets produced from the Iron Mountain site in Northern California and customized tools, researchers used bacterial spacer sequences commonly called CRISPRs to link phage and hosts in ecological studies. The Impact: Interactions between uncultivated microbes and their phage… [Read More]

A Single-Cell Pipeline for Soil Samples

Scientists evaluate a process that uses NanoSIMS and Raman microspectroscopy for in situ microbial studies. The Science: To investigate in situ function of uncultivated microbes, scientists evaluated a process for preparing soil samples for single-cell analysis methods. The Impact: The process allows researchers to efficiently analyze microbial activities at the single-cell level in soil systems,… [Read More]

Expanding Barley Genetics Resources

Genomic regions containing two-thirds of all annotated barley genes have been sequenced. The Science: Researchers generated nearly 16,000 sequences of gene-containing regions for barley, mapping approximately two-thirds of all annotated barley genes. The Impact: While researchers continue to work on a complete reference sequence for the barley genome, the determination of improved sequence assemblies for… [Read More]

Seeking “Gold Standard” Wastewater Treatments

Metagenomic analyses lend insights into how microbes break down wastewater contaminants. The Science: Researchers conducted analyses of microbial communities in laboratory-scale bioreactors breaking down contaminated wastewater from gold ore processing. The Impact: In this “first application of genome-resolved metagenomics” to characterize bioreactors involved in gold ore processing, the data reveal how the bioreactors utilize available… [Read More]

First Public Resource for Secondary Metabolites Searches

IMG-ABC allows researchers to link sequencing data and the search for novel biosynthetic gene pathways. The Science: The wealth of genomic and metagenomic datasets for microbes, particularly from previously unstudied environments, within the Integrated Microbial Genomes (IMG) system is being applied in a new public database to the search for novel secondary metabolites that could… [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]

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]

Charting Short-Term Results of Wetlands Restoration

Patterns in carbon sequestration and emissions are charted in the San Joaquin Delta. The Science: Researchers at the DOE Joint Genome Institute sequenced and analyzed the microbial communities in restored wetlands in the Sacramento-San Joaquin Delta and combined the data with greenhouse gas measurements from the area to track patterns in methane emissions. The Impact:… [Read More]

The Most Complete Functional Map of an Entire Enzyme Family

DOE-funded researchers develop a new process for annotating cellulose-degrading enzymes. The Science: Researchers at two Department of Energy-funded Scientific User Facilities collaborated with one of three Bioenergy Research Centers to develop and analyze high-resolution crystal structures of an enzyme from the cellulose-degrading GH55 family. They then went further and were able to apply a variety… [Read More]

Understanding the [Non-Coding] Spaces Between

DOE JGI researchers sequenced and analyzed a cyanobacterium with known nitrogen-fixing capabilities. The Science: Researchers sequenced and analyzed the uncommonly large genome of a nitrogen-fixing cyanobacterial strain, comparing it to the more than 150 extant cyanobacterial genomes. The Impact: Unlike many of the existing cyanobacterial genome sequences, the genome of Trichodesmium erythaeum IMS 101 is… [Read More]