The total allocation for the coming year’s CSP portfolio will exceed 30 trillion bases (terabases or Tb), a 100-fold increase compared with just two years ago, when just a third of a terabase was allocated to more than 70 projects. This amounts to the equivalent of at least 10,000 human genomes in data.

These selections truly take advantage of the DOE JGI’s massive-scale sequencing and data analysis capabilities. The projects span the globe and the unexplored branches of the tree of life, and promise to yield a better understanding of the interplay between climate, ecosystem and organism. Still other projects are targeting improvements in biofuel feedstock production, focusing on the potential of microorganisms to improve feedstock growth and prevent devastating diseases that hinder yields.

—Eddy Rubin, DOE JGI Director

One of single largest projects comes from Jeff Dangl at the University of North Carolina and his colleagues and focuses on the rhizosphere—the narrow region where microbes in the soil colonize and interact with plant roots. The importance of rhizosphere microbial communities for plant growth and success cannot be overstated.

The distinctive ‘terroir’ that flavors wine, the yield of maize and other crops, and the productivity of any plant community rely in part on the respective rhizosphere microbiome. The microbiome is most simply viewed as an extension of each plant’s genome; we do not know any plant genome’s full functional capacity until we also know the functional capacity and the drivers governing assembly of its associated microbiome.

—Dangl team proposal

The Dangl team seeks to apply the genetic and genomic information toward applications in bioenergy and carbon cycling research. They propose to study the rhizosphere microbiomes of maize, Arabidopsis and a mustard relative known commonly as Drummond’s rockcress, as well as potential biofuel crop Miscanthus and wild prairie grasses, to understand the plant genetics involved in determining the microbial communities associated with plant species.

A few of the other projects include:

• Casuarina trees are able to tolerate soils laden with salt and heavy metals due to Casuarina symbiosis with Frankia bacteria. As these trees have the potential to serve as biomass sources in tropical and subtropical regions of the world, the team led by Laurent Laplaze from the French institute IRD-Montpellier proposes to use deep sequencing to analyze gene expression changes in the roots and nodules of the Casuarina trees and learn more about how these plant-microbe interactions influence nitrogen fixation and carbon sequestration.

• A team led by Joseph Spatafora at Oregon State University and Jason Stajich at University of California at Riverside is planning to fill in gaps in the Fungal Tree of Life by sequencing 1,000 fungal genomes over the next five years, providing at least two reference genomes for each of the 577 recognized families classified under Fungi.

• Another fungal project approved this year was proposed by US Department of Agriculture researcher Jo Anne Crouch and involves several species of the grass-infecting fungus Colletotrichum. As more grasses are explored as candidate bioenergy feedstocks, strategies that defend against fungal pathogens that may reduce plant biomass and thus yields of cellulosic biofuels are of particular interest. Additionally, novel enzymes in these fungal genomes may have industrial applications in the biomass pretreatment processes.

• Thomas Brutnell and Todd Mockler of the Danforth Plant Science Center will develop sequence-based community tools for Setaria viridis—a model genetic system for bioenergy grasses. Setaria is rapidly emerging as a model system for bioenergy grasses as it is closely related to the primary bioenergy feedstock crops such as switchgrass, Miscanthus and sugarcane, but is a much more manageable genetic system. This project will include providing sequence blueprints for more than 50 diverse varieties of Setaria as well as providing the data to facilitate the development of mutagenized populations and lines that can be used to map genetic variation. The development of these genetic resources will enable scientists to identify genes that contribute to a number of traits that are essential to develop efficient biomass production including increased stress tolerance, water and nitrogen use efficiency and biomass production.

• Samuel Hazen at the University of Massachusetts will lead a team to create a library of grass transcription factors for the energy crop model system Brachypodium distachyon. Brachypodium serves as a model for potential energy crops such as switchgrass, sorghum, and Miscanthus, as well as for the cereal crops that constitute a large part of the world’s diet. Transcription factors are proteins that regulate gene expression, and the Brachypodium transcription factors targeted in this project are implicated in grass cell wall biosynthesis and the regulation of growth and biomass accumulation by light.

• Another terabase-sized metagenome project comes from Craig Cary at the University of Delaware and Charles Lee at the University of Waikato in New Zealand. Their plan focuses on the microbial communities in the McMurdo Dry Valley system of Antarctica. Considered to be among the harshest and most extreme environments on the planet with low water and nutrient levels paired with high salt and ultraviolet radiation levels, the team seeks to understand how the carbon cycle plays out in this ecosystem. Additionally, the microbes in this environment may offer insight into bioremediation applications for cold ecosystems.

• The first genomic characterization of a microbial community resulted from a collaboration between the DOE JGI and Jill Banfield at the University of California, Berkeley and her colleagues and involved samples from a US Environmental Protection Agency Iron Mountain Superfund site in Northern California. Now Banfield and her colleagues propose to recover genomes from subsurface microbial communities at the DOE Integrated Field Research Challenge bioremediation research site at Rifle, Colorado. They will generate, initially, a terabase of sequence to identify novel rare microbes that might be useful for the environmental cleanup of metals and radionuclides, and which may also lend insight into subsurface carbon sequestration.

• A team led by Michael Pester from the University of Vienna in Austria proposed one of the CSP 2012 portfolio’s smaller sequencing projects. They propose to work with roughly 100 Gb of metagenome and metatranscriptome (the region of the complete genetic code that is transcribed into RNA molecules and provides information on gene expression and gene function) sequence to study the greenhouse gas emissions from the microbial communities that reside in peatlands, a significant carbon sink. The researchers noted that peat soil contains methane-producing organisms whose emissions are mitigated by poorly-studied sulfate reducing microbes.