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DOE Joint Genome Institute approves 41 projects for 2012 Community Sequencing Program; climate, environment and bioenergy feedstocks

The US Department of Energy (DOE) Joint Genome Institute (JGI) has approved 41 projects from 152 submitted (culled from the 188 letters of intent originally received) for the 2012 Community Sequencing Program (CSP). The 2012 Community Sequencing Program (CSP) call invited researchers to submit proposals for projects that advance capabilities in fields such as plant-microbe interactions; microbes involved in carbon capture and greenhouse gas emission; and metagenomics—the characterization of complex collections of microbes from particular environmental niches.

In an indication of the increasing use of sequencing to study whole biological systems rather than individual organisms, more than half the approved proposals include sequencing of multi-organism samples either instead of or in addition to individual genomes. Of the proposals that include individual genome sequencing, nine address plant genomes; six are fungal projects; and eight are microbial projects, five of which involve sequencing the genomes of single cells.

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.

Community Sequencing Program Sequencing Plans for 2012
Proposer Affiliation Project Description
Acinas, Silvia ICM-CSIC, Spain Microbial metagenomics and transcriptomics from a global deep-ocean expedition
Andresson, Olafur University of Iceland Sequencing of the three cultured partners of the lichen Lobaria pulmonaria and the sequencing of the transcriptomes from the natural tripartite lichen under selected and controlled conditions.
Banfield, Jill University of California, Berkeley Terabase sequencing for comprehensive genome reconstruction to assess metabolic potential for environmental bioremediation
Brodie, Eoin DOE JGI Mediterranean Grassland Soil Metagenome (MGSM): Enabling a systems view of soil carbon and nitrogen biogeochemistry under a changing climate.
Brutnell, Thomas Boyce Thompson Institute for Plant Research Development of sequence-based community tools for Setaria viridis-a model genetic system for C4 grasses
Bucking, Heike South Dakota State University Exploring the transcriptome of perennial grasses in association with beneficial microorganisms to increase biomass production and environmental sustainability of bioenergy production
Cary, Stephen University of Delaware Understanding terrestrial microbial biocomplexity in an Antarctic desert landscape: resolving universal drivers of community structure and function in a trophically simple system
Crouch, Jo Anne USDA-ARS Genomic signatures of pathogenicity and endophytism in five species of grass-associated Colletotrichum impacting the health and production of bioenergy feedstocks, agriculture and the environment
Dangl, Jeff University of North Carolina at Chapel Hill Plant associated metagenomes--Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems.
DeAngelis, Kristen University of Massachusetts Microbial ecology and genomics of carbon-storing bacteria in rhizosphere soils
Dubilier, Nicole Max Planck Institute for Marine Microbiology, Germany Understanding novel pathways for energy and carbon use in bacterial symbionts of gutless marine worms
Emerson, David Bigelow Laboratory for Ocean Sciences Single cell genome sequencing of biomineralizing bacteria
Fierer, Noah University of Colorado Cross-site metagenomic analyses to assess the impacts of experimental nitrogen additions on below-ground carbon dynamics
Fredrickson, Jim Pacific Northwest National Laboratory Microbial Interactions in Extremophilic Mat Communities
Gilbert, Jack Argonne National Laboratory Creating a successional model for carbon remediation in the Gulf of Mexico
Gross, Stephen DOE JGI The Agave Microbiome: Exploring the role of microbial communities in plant adaptations to desert environments
Hazen, Samuel University of Massachusetts Creating a multi-functional library of grass transcription factors for the energy crop model system Brachypodium distachyon
Hess, Matthias Washington State University Expression profile of biomass-degrading fungi inhabiting the cow rumen
Kelly, William AgResearch, New Zealand The Hungate 1000. A catalogue of reference genomes from the rumen microbiome.
Kerfeld, Cheryl DOE JGI Enhancing Bacterial Carbon Capture and Sequestration: Synthesis of Building Blocks for the Carboxysome, A Metabolic Module for CO2 Fixation
Kyrpides, Nikos DOE JGI Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project
Laplaze, Laurent Institut de Recherche pour le Développement (IRD), France Transcriptome Analysis of Salt Tolerance in Casuarina trees
Martin, Francis INRA, France Metatranscriptomics of Soil Forest Ecosystems
McKay, Robert Bowling Green State University Metagenomics and metatranscriptomics of the Lake Erie ‘dead zone’: a seasonal source of greenhouse gases
McMahon, Katherine University of Wisconsin, Madison Dynamics of microbial carbon processing pathways across a decade in a freshwater eutrophic lake revealed through metagenomic sequencing
Mock, Thomas University of East Anglia, UK Sea of Change: Eukaryotic Phytoplankton Communities in the Arctic Ocean
Mohn, William University of British Columbia, Canada Metagenomic and metatranscriptomic analysis of forest soil communities across North America
Moran, Mary Ann University of Georgia The Genetic Basis for Heterotrophic Carbon Processing in the Sea
Murray, Alison Desert Research Institute Lake Vida brine microbial community (LVBMCo) genomics and transcriptomics - a window into diversity, adaptation and processes in extreme cold
Muyzer, Gerard Delft University of Technology Genome sequencing of 100 strains of the haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacterium Thioalkalivibrio
Nealson, Kenneth University of Southern California Life at the edge: community cooperation and success in a very extreme (ultrabasic and ultra-reducing) environment
Ohm, Robin DOE JGI Towards functional genomics: development of Schizophyllum commune as a model system to study lignocellulose degradation
Pester, Michael University of Vienna, Austria Targeted metagenomics and metatranscriptomics of a sulfate-reducing rare biosphere member and potentially novel sulfate reducers that impact methane emission from peatlands
Powell, Amy Sandia National Laboratories A Phylogenomic Framework to Investigate Fungal Thermophily
Pukkila, Patricia University of North Carolina at Chapel Hill Functional genomics in the model mushroom Coprinopsis cinerea
Rodrigues, Jorge University of Texas at Arlington Profiling metagenomic consequences of Amazon deforestation at different spatial scales
Schadt, Christopher Oak Ridge National Laboratory Defining the Populus Microbiome: Role of Genotype by Environment Interactions in Shaping the Rhizosphere Microbiome of Populus trichocarpa
Schrenk, Matthew East Carolina University Metagenome-enabled Investigations of Carbon and Hydrogen Fluxes within the Serpentinite-hosted Subsurface Biosphere
Spatafora, Joseph Oregon State University 1000 Fungal Genomes
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Dark ocean microbial single cell genomics
Wing, Rod University of Arizona Empowering functional plant genomics with genomes and transcriptomes of the top 20 Brassicales

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