Soil microbes carry out life-sustaining functions for our planet, including promoting plant growth. ESD’s Janet Jansson et al. are using a metagenomics approach to better understand soil microbes and their functions.
Researchers in the United States, Europe, and elsewhere are doing metagenomic analyses on a wide variety of soil samples from different climates, regions, and conditions.
Here, the term metagenome refers to sequencing of total community DNA, including both phylogenetic and functional genes, while taking a shotgun-sequencing approach. Although few shotgun soil metagenome studies are published, more are anticipated during the next year (Table 1) as investigators take advantage of recent advances in sequencing instruments, for example, using 454 pyrosequencing and Illumina technologies.
Combining “omics” approaches with cultivation and single-cell sequencing will help to address fundamental questions about soil microbial ecology.
Although investigators are learning a great deal about dominant bacteria and archaea in soils based on 16S rRNA gene sequence data, many of the dominant operational taxonomic units (OTUs) that we detect in soil have no close representatives in culture collections. Researchers are addressing these deficiencies through initiatives such as the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project that Jonathan Eisen of the University of California, Davis (UCD) and JGI coordinates.
Better algorithms, new bioinformatics tools, and “terabytes” of computer storage are required to accommodate metagenomic sequence data from analysis of soil samples.
Jillian Banfield studies very, very small things, but her work is vast in its scope and impact. So vast, in fact, that her discoveries have implications for space, the human body and nearly everything in between.
“Sit Down With Sabin” is a summer lecture series, during which former San Francisco Chronicle science reporter and current Lab employee Sabin Russell interviews innovative scientists about their research. This video is the third installment; a talk with ESD's Margaret Torn.
Find out what you missed happening around ESD during June 2011! This digest includes new ways to stay connected to ESD, publication list updates, new hires, and research highlights.
The first two weeks of June 2010 were a blur for six scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). As the world focused on the ongoing crisis in the Gulf of Mexico after the blowout of BP’s Deepwater Horizon Macondo well, the scientists dropped everything to estimate how much oil was flowing from the mangled wellhead.