Terragenomics: The Argonne pilot project for a comprehensive National Soil Metagenomics Project
Argonne has started a pilot project for a comprehensive metagenomics study of the nations soil. DNA sequence data for the microorganisms The project database will contain sequence data (metagenomes) and additional information pH, soil use, elemental cycling for approx. 50 different soil types across the U.S. The aim of this project is launch a larger effort for the comprehensive characterization of the microbial content in our nation's soils as the first step in understanding community composition, elemental cycling (including carbon, nitrogen, sulfur, and phosphorus), and secondary metabolism.
Understanding microbial carbon cycling is essential to develop approaches to enhance biological carbon sequestration to offset carbon dioxide emissions. Recent studies suggest that microbial carbon sequestration (by bacteria, Archaea, and small algae) may exceed that from the macrobial ecology (plants, trees, etc). Understanding nitrogen cycling in the soil will increase the security of the food supply chain by potentially reducing the need for fertilizers. An average hectare of agricultural land is supplemented with approximately 150 kg of nitrogen-based fertilizer per year, however recent studies suggest that microbes in the soil may just oxidize a large fraction of the nitrogen applied before it can benefit the plants. By comparing the microbial soil composition nationwide, we will begin to determine the keystone microbes in different environments, and their contributions to the global carbon, nitrogen, and sulfur cycles.
The project will begin sampling at approximately 50 field sites, and at every location we are going sequence two samples of DNA. The DNA will be extracted from the microbial fraction of the soil without cloning or amplification. Every sampling location will be described by temperature, pH, land-use type etc. The sites with be characterized by GPS to precisely define the location, we will also add soil respiration data using a mobile CO2 turnover testing device. We will also accept soil and/or DNA samples from researchers nationwide for inclusion in the program.
A open, comprehensive, web enabled knowledge-base will be set up that makes all data and subsequent analyses immediately available. All data will be also available for download. The first metagenome data sets will be made available in spring of 2008.
* Sequencing of the first metagenome samples
Bioinformatics (R. Edwards, F. Meyer, D. Paarmann)
Sequences will be analyzed using the high-performance SEED metagenomics-RAST server (http://metagenomics.theseed.org/) to identify both functional and taxonomic profiles. This service, developed by researchers in the Mathematics and Computer Science Division, will allow us to immediately identify the key microbial components of each metagenome, and characterize the metabolism in each environment.
Sequencing (M. Domanus, K. White)
The newly established ANL sequencing core within the Institute for Genomics and Systems Biology will provide a random community genome (metagenome) sequence for every sample using a pyrosequencing approach.
Soil Ecology (J. Jastrow, R. Matamala, R. Miller)
The Terrestrial Ecology group will not only provide their expertise in site selection, sample preparation, DNA extraction but also provide support measuring other parameters like pH, C, N, P, ..