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Genomics of Energy & Environment User Meeting Abstracts DEPARTMENT OF ENERGY JOINT GENOME INSTITUTE (DOE JGI) Genomics of Energy & Environment User Meeting Abstracts March 26–28, 2013 / Walnut Creek Marriott / Walnut Creek, CA An electronic version of this document is available at: http://go.usa.gov/g3P All information current as of March 14, 2013 JGI Contact: Marsha Fenner DOE Joint Genome Institute [email protected] The Joint Genome Institute is a user facility of the Department of Energy Office of Science DOE Joint Genome Institute: www.jgi.doe.gov DOE Office of Science: science.doe.gov Eighth Annual DOE Joint Genome Institute User Meeting Sponsored By U.S. Department of Energy Office of Science March 26-28, 2013 Walnut Creek Marriott Walnut Creek, California Contents Speaker Presentations .................................................................................................................................. 1 Poster Presentations ..................................................................................................................................... 8 Attendees .................................................................................................................................................... 58 Author Index ............................................................................................................................................... 64 Speaker Presentations Abstracts alphabetical by speaker Assembly-driven metagenomics of a hypersaline microbial ecosystem Eric E. Allen ([email protected]) Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California; Division of Biological Sciences, University of California at San Diego Microbial populations inhabiting a natural hypersaline lake ecosystem, Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo sequence assembly, and multidimensional phylogenetic binning. Consensus genomes were reconstructed for twelve environmental microbial populations, eleven archaeal and one bacterial, comprising between 0.6-14.1% of the planktonic community. Eight of the twelve genomes recovered represent microbial populations not characterized previously in laboratory culture. The extent of genome assembly achieved has allowed extensive lineage-specific compartmentalization of predicted metagenomic functional capabilities and cellular properties associated with both dominant and less abundant members of the community. The generation of habitat-specific, environmental reference genomes based on metagenomic sequence assembly provides rich opportunities for discovering the genetic architecture of multiple microbial groups constituting a native microbial ecosystem. The degree of connectivity between microbial populations based on metabolic network analysis reveals exquisite functional redundancy in hypersaline microbial communities. This constrained metabolic repertoire may reflect limitations of adaptation to extreme salinity and is consistent with the hypothesis that temporal variability in community membership may be dominated by top-down forcing dynamics (e.g. grazing and viral predation) rather than nutrient availability and assimilation. Regulation of flowering in Brachypodium distachyon Richard Amasino ([email protected]) University of Wisconsin, Madison, Wisconsin The major developmental change in the plant life cycle is the initiation of flowering. Upon the initiation of flowering, many plants do not produce much additional cellulosic biomass for the remainder of the growing season. The initiation of flowering is often a response to sensing seasonal change—for example sensing changes in day-length and temperature. We are using a genetic approach to identify genes that are involved in the timing of flowering in the model grass Brachypodium distachyon, with a focus on vernalization—the acquisition of competence to flower after prolonged exposure to winter cold. Although work from our group and others has revealed much about the molecular nature of vernalization in the crucifer Arabidopsis thaliana, grasses have a vernalization system that evolved independently of that in Arabidopsis thaliana. In fact, the vernalization systems in different groups of plants result from convergent evolution because when flowering plants were diverging there was not an advantage to possessing vernalization systems—the Earth was much warmer and the landmasses were in different locations than at present. Our study of biomass traits in Brachypodium distachyon is supported by the Great Lakes Bioenergy Research Center (www.glbrc.org/). Speaker Presentations Network as discovery instrument: A quick-start guide Greg Bell ([email protected]) DOE ESnet, Lawrence Berkeley National Laboratory, Scientific Networking Division, Berkeley, CA Scientific progress should not be constrained by the physical location of instruments, people, computational resources, or data. Advanced research networks are now making steady progress at achieving that vision. In this talk, ESnet's Greg Bell will attempt to raise your expectations for networks; explain how they can accelerate scientific workflows; and provide guidance about getting maximum benefit from ESnet, Internet2, or whichever research network serves your home institution. The Isthmus of Panama — A natural laboratory for the genomics of climate resilience Eldredge Bermingham ([email protected]) Smithsonian Tropical Research Institute, Washington, D.C. The Isthmus of Panama joined the continents of North and South America roughly 3 million years ago, and separated the modern Caribbean Sea from the Eastern Pacific Ocean. This event established an interchange of terrestrial biodiversity of epic proportions between the continents, and initiated the genomic divergence of marine organisms separated by the isthmus. Moreover, the narrow isthmus spans a two-fold rainfall gradient in the 300,000-hectare Panama Canal Watershed, and is impacted by El Niño and La Niña. The environmental attributes of Panama, coupled to the 100-year presence of the Smithsonian Tropical Research Institute on the Isthmus, create a remarkable opportunity to use genomic approaches to understand diversity and climate resilience in organisms ranging from the coral holobiont to the mosaic genomes of rain-forest trees. Single-cell genomics of environmental bacteria Paul Blainey ([email protected]) Broad Institute Succession of microbial phylogeny and function during plant litter decomposition Eoin L. Brodie ([email protected]) and Mari Nyyssonen Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California Trait-based models that connect microbial composition to ecosystem functioning typically represent microorganisms as functional guilds or groups of organisms sharing similar trait combinations. Key to this approach is the need to constrain trait combinations to avoid the emergence of so called ‘Darwinian demons’ – an organism that maximizes all fitness traits. Advances in environmental metagenomics now permit reconstruction of complete genomes from complex microbial communities, potentially enabling trait distributions and trait combinations to be defined or at least constrained. Abstracts alphabetical by speaker 2 Speaker Presentations However, this approach is largely dependent on in silico gene predictions and is facilitated by characterized microbial isolates of limited diversity and environmental distribution – which may result in an underestimation of functional diversity and redundancy. Parallel function-based mining of metagenomic libraries can provide direct linkages between genes and metabolic traits and thus bridge the gap between sequence data generation and functional predictions from environmental genomic datasets. We have developed high-throughput screening assays for function-based characterization of activities related to plant polymer decomposition contained in environmental metagenomes. The multiplexed assays are based on fluorogenic and chromogenic substrates and combine automated liquid handling and a genetically modified expression host to enable the daily screening of 12,160 fosmid clones against 13 substrates in more than 170,000 reactions. To illustrate the utility of the developed assays, we analyzed leaf litter metagenomic fosmid libraries sampled during litter decomposition. Positive clones were sequenced using the MiSeq platform for identification of genes conferring the observed activities and associated traits. Merging these data with shotgun metagenomic sequence data allows the genomic context of these traits to be determined and the linkage of additional functional traits. Strange tails in viral discovery Joseph DeRisi ([email protected]) Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California Synthetic metagenomics: Converting digital information back to biology Samuel Deutsch ([email protected]) DOE Joint Genome Institute, Walnut Creek, California Next-generation sequencing technologies have enabled single genomes as well as complex environmental samples (metagenomes) to be sequenced on a routine basis. Bioinformatics analysis of the resulting sequencing data reveals a continually expanding catalogue of predicted proteins (> 50 million), which cover the full spectrum of known pathways and functional activities. Converting sequencing data retrieved from databases (digital information) into biochemical molecules that can be functionally characterized remains challenging
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