THE 11TH ANNUAL DOE Joint Genome Institute Genomics of Energy & Environment Meeting March 21-24, 2016 • Walnut Creek Marriott • Walnut Creek, California User Meeting Abstracts All information current as of March 15, 2016 JGI Contact: Denise Yadon 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.energy.gov THE 11TH ANNUAL DOE Joint Genome Institute Genomics of Energy & Environment Meeting March 21-24, 2016 • Walnut Creek Marriott • Walnut Creek, California User Meeting Abstracts Sponsored By U.S. Department of Energy Office of Science Table of Contents Speaker Presentations .....................................................................................................1 Poster Presentations ......................................................................................................10 Index ..............................................................................................................125 Attendees ..............................................................................................................135 Speaker Presentations Speaker Presentations Abstracts alphabetical by speaker The Nature of Scientific Publishing Bahcall, Orli* ([email protected]) Nature. Tara Oceans: Eco-Systems Biology at Planetary Scale Bowler, Chris* ([email protected]); Tara Oceans Consortium Ecology and Evolutionary Biology Section, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Paris, France. The ocean is the largest ecosystem on Earth and yet we know very little about it. This is particularly true for the plankton that drift within. Although these organisms are at least as important for the Earth system as the forests on land, most of them are invisible to the naked eye and thus are largely uncharacterized, even though they form the base of marine food webs. To increase our understanding of this underexplored world, a multidisciplinary consortium, Tara Oceans, was formed around the 110-ft research schooner Tara, which sampled plankton at more than 210 sites and multiple depth layers in all the major oceanic regions during expeditions from 2009-2013 (Karsenti et al. Plos Biol., 2011). The seminar will describe the first foundational resources from the project (based on a first data freeze from 579 samples at 75 stations; see Science special issue May 22, 2015) and their initial analyses, illustrating several aspects of the Tara Oceans’ eco-systems biology approach. The project provides unique resources for several scientific disciplines, capturing biodiversity of a wide range of organisms that are rarely studied together, exploring interactions between them and integrating them with environmental conditions to further our understanding of life in the ocean and beyond in the context of ongoing climate changes. Deep Sequencing Methods for Detecting Infectious Agents Chiu, Charles* ([email protected]) University of California, San Francisco. Abstracts alphabetical by speaker 1 Speaker Presentations Genetic Basis of Competitive Success and Priority Effect Exhibited by Dominant Nectar Yeast, Metschnikowia reukaufii Dhami, Manpreet* ([email protected]) Stanford University, Stanford, California, USA. Floral nectar hosts a complex community of microbes. Floricolous yeast, Metschnikowia reukaufii, is a dominant species in this community, competing with other fungi and bacteria. Specifically, this species exerts a strong priority effect, excluding other microbes and deterministically influencing community structure. Sequencing and analysis of the M. reukaufii genome revealed a putative genetic mechanism by which it specialises in nectar. We found high rates of tandem gene duplication, which were enriched for nitrogen metabolism and transport. The two major high capacity amino acid transport (HCAT) genes, involved in amino acid scavenging when nitrogen is scarce, were present in tandem gene arrays. These additional HCATs are expressed under nectar conditions but repressed if nitrogen is abundant. We propose that M. reukaufii evolved the ability to rapidly and efficiently deplete amino acid from nectar, limiting the growth of subsequently arriving microbes, while protecting itself from osmotic stress and explains the strong priority effect and competitive success exhibited by M. reukaufii. The Divining Root: Understanding How Roots Find Water in a Heterogeneous Environment Dinneny, Jose* ([email protected]) Carnegie Institution for Science. While plants are sedentary, their bodies often traverse long distances as they explore their local environment in search of resources necessary for growth. The biology of root systems is governed by both micro-scale and systemic signaling that allows the plant to integrate these complex variables into growth and branching decisions that ultimately determine the efficiency with which resources are captured. Research in my lab is aimed at understanding the response of roots to water-limiting conditions and is exploring this process at different organizational scales from the individual cell type to the level of the whole plant. Mining Genomes for Producing Fuels and Chemicals from Biomass Donohue, Tim* ([email protected]) University of Wisconsin-Madison. Great Lakes Bioenergy (www.glbrc.org) is one of three Department of Energy funded Bioenergy Research Centers conducting genome-enabled, systems level research to provide the underpinnings for production of fuels and chemicals from the lignocellulosic, or non-edible, fraction of plant biomass. To achieve its mission, GLBRC basic science activities are led by academic and national lab scientists (University of Wisconsin-Madison, Michigan State University, University of British Columbia, Texas A&M Abstracts alhpabetical by speaker 2 Speaker Presentations University, Illinois State University, University of New Hampshire, University of Maryland and Pacific Northwest National Lab) who are focused on providing knowledge toward the sustainable production of crops with desirable biofuel traits and energy efficient conversion of biomass into fuels and chemicals. The Center’s research portfolio is built on integrated, discovery research activities in Sustainability: to identify factors affecting the ecological attributes of biofuel cropping systems, Plants: to improve the traits and productivity of bioenergy crops, Deconstruction: to improve chemical and enzymatic methods for solubilizing lignocellulosic biomass, and Conversion: to improve microbial and chemical systems for converting materials derived from lignocellulosic biomass to biofuels and chemicals. Since its inception in 2007, Great Lakes Bioenergy has reported findings in >850 papers, produced knowledge that led to filing ~125 patents, licenses for ~3 dozen technologies, and formation of several start-up companies. This talk will report on several projects that have used high-throughput sequencing to mine plant and microbial genomes for the production of cellulosic biofuels. Microbial Drivers of Cellulose Cycling in Biofuel Crop Soils Hofmockel, Kirsten S.* ([email protected])1,2; Erb, Racheal1; Bell, Sheryl1; Christer, Will2; Thompson, Allison1; Brown, Joe1; Bramer, Lisa1; Orr, Galya2 1Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA. 2Iowa State University, Ames, IA. We examined the microbial interactions and metabolic functions involved in the degradation of cellulose in enrichment cultures derived from biofuel agroecosystem experiments. To identify key organisms and enzymes involved in root decomposition, we used fluorescently labeled cellulose nanocrystals in combination with metatranscriptomics in controlled enrichment experiments. We demonstrate that the community level responses (OD, respiration, 16S amplicons) were not significantly different when soil communities were grown with cellulose or fluorescently labeled cellulose nanocrystals over a 10d incubation, suggesting our experimental platform can be used to track the fate of cellulose through soil decomposer communities. Our results reveal that Proteobacteria, which represent 10% of the native soil community, dominated the community in our cellulose degrading experiments, comprising 32% of the enrichment culture and 80% of the community by day 10. Pseudomonadales were the most abundant, increasing from 2% of the community to greater than 50% during the cellulose enrichment experiment. Organisms assimilating the fluorescently labeled cellulose have been analyzed in conjunction with metatranscriptomic data to understand the basic ecology regulating cellulose decomposition in diverse soil communities. By targeting extracellular enzymes typically measured in biogeochemical field studies and organisms native to the soil community, we aim to link reduced lab studies to field approaches and predictive models. This research was supported by the Genomic Science Program, U.S. Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DESC0010775. This work was part of the FICUS, EMSL-JGI user program. Abstracts alphabetical by speaker 3 Speaker Presentations Pleiotropic and Epistatic Network-Based Discovery: Integrated SNP Correlation, Co-expression and Genome-Wide Association Networks for Populus trichocarpa Jacobson, Daniel* ([email protected])1,2; Weighill, Deborah1,2; Bleker, Carissa1,2; Tuskan, Gerald1; Muchero, Wellington1; Tschaplinski,