Source: Janet Jansson
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.
In a project involving Janet Jansson’s team at LBNL, James Tiedje and his colleagues at Michigan State University, and the Joint Genome Institute (JGI), investigators are using a combination of second-generation platforms to sequence DNA from microbes in soil samples from the Great Prairie of the United States, including native prairie and adjacent cultivated soils from Wisconsin, Iowa, and Kansas (Table 1). This project aims to determine the impact of land management (tillage, fertilization, etc.) on soil microbial communities and their functions, including cycling of carbon and nitrogen. One of the sites, Kansas native prairie, is also the focus of another project that is specifically addressing the impact of altered rainfall patterns due to climate change on carbon cycling processes in the Great Prairie. The Kansas prairie metagenome that was sequenced at JGI currently has the largest amount of sequence data of any soil metagenome to date, approaching 400 Gb of Illumina sequence, and will serve as a resource for this project.
Also in collaboration with JGI, Jansson’s team sequenced DNA extracted from Alaskan permafrost soil samples collected by Mark Waldrop from the U.S. Geological Survey (USGS). The aim for this work is to use metagenomics to gain an understanding of the impact of climate warming-induced thaw on the microbial degradation of carbon reserves that have been trapped in permafrost for thousands of years and that have potential to contribute large amounts of greenhouse gases to the atmosphere. Other ongoing soil metagenome sequencing projects include several that focus on field sites for which there is substantial temporal environmental and climate data. For example, the UK Rothamsted Field Station is one of the longest running field stations in the world and has served as the site for several metagenome sequencing projects. One of these projects, "Deep-Soil" (Table 1), is sequencing DNA from a long-term grassland and an adjacent fallow site at Rothamsted. The overarching goal of this sequencing effort is to establish the long-term impact of plants on the soil microbiota. Another project at Rothamsted is a French metagenome sequencing project, Metasoil, coordinated by Tim Vogel and Pascal Simonet of the Ecole Centrale de Lyon, France. The Metasoil project is sequencing DNA from the Park Grass site at Rothamsted that was established in 1856. Their strategy relies on constructing and sequencing a fosmid library in addition to shotgun metagenome sequencing. In further collaboration with JGI, Cheryl Kuske and coworkers at the Department of Energy (DOE) Los Alamos National Laboratory are sequencing soils from selected free air-carbon dioxide enrichment (FACE) sites in the United States. These sites were established to determine the influence of increases in atmospheric CO2 levels due to climate change on terrestrial ecosystems. In addition, Folker Meyer and coworkers at the DOE Argonne National Laboratory are sequencing metagenomes from several different U.S. soils that were collected across a range of habitats to determine which microorganisms and functional processes predominate in different soil ecosystems.
Another approach is to sequence subsets of the metagenome, such as collections of ribosomal RNA (rRNA) signature sequences. For example, based on 16S rRNA gene sequence data, Janet Jansson’s team has developed a relatively good understanding of the species diversity and distribution of specific bacterial and archaeal phyla in different soils. Further, based on work from Noah Fierer, Rob Knight, and their colleagues at the University of Colorado, Boulder, pH and salinity have been established as major drivers of microbial biogeography. These and other studies have shown that soils contain high abundances of Acidobacteria, whose 26 subgroups vary in abundance from one soil type to another. Also, some phyla are more prevalent in a given soil type than in others. More generally, databases of 16S sequences are yielding insights into how chemical and physical parameters correlate with microbial distributions in soils.
Together, these soil metagenomics projects will be a tremendous resource to the scientific community and will provide a much greater understanding of microbial diversity and functions in soil.