Department of Energy Washington, DC 20585 February 26, 2018 Dear Colleague: On behalf of the Biological Systems Science Division (BSSD) welcome to the 2018 Genomic Science Annual PI Meeting! I’d like to thank you for your efforts over the past twelve months in continuing to focus on your research and delivering the scientific results needed by this program, the Department and the Nation. Your work is vital and important and we thank you. This past year has been marked by significant challenges but also remarkable progress. While there’s no denying the considerable uncertainty with the Federal Budget process we have nonetheless continued to make necessary changes within the program to keep the research forward-looking and fresh. Over the past year we’ve initiated four new Bioenergy Research Centers, a new and expanded set of Biosystems Design projects, continued our efforts in Plant Feedstocks research and initiated new Microbiome projects at the DOE Labs. We are currently reconfiguring our computational biology and bioinformatics systems to a more open access format and developing new and/or improved Bioimaging capabilities for the portfolio. In short, we have continued to align and refresh the portfolio to help meet DOE’s basic science goals for bioenergy and environmental research. As in past meetings this annual event is an opportunity to view the entire program and to see where your project fits in with the larger portfolio. All funded principal investigator projects from our University portfolio and the DOE National Laboratory portfolio are present at this meeting. I would urge all researchers to take full advantage of the opportunity to meet your colleagues. You would be hard pressed to find a more focused scientific group in which to discuss your ideas for DOE research. This is also an opportunity to meet with your DOE program staff, representatives from elsewhere within the Department of Energy, and colleagues from other Federal Agencies. Within BSSD we also strive to develop new and enabling research capabilities within the programs and at the DOE User Facilities. At this meeting there will be plenary and poster presentations of a variety of enabling capabilities supported within BER including the DOE Joint Genome Institute (JGI), the Environmental Molecular Science Laboratory (EMSL), the DOE Synchrotron Light and Neutron Sources and, the DOE Systems Biology Knowledgebase (KBase). Investigators from the Bioimaging research portfolio are also in attendance and will participate in the Bioimaging Research annual PI meeting immediately following this meeting. I would urge you to visit with representatives of these facilities/projects to learn more about new and/or upcoming capabilities available to you as a researcher. We have planned a full agenda highlighting the exceptional research results produced within the program over the past year. We hope that these presentations will spark fruitful discussions that can be carried into the poster sessions, which are the heart of this meeting. The Bioenergy Research Center program has launched its 11th year with four new BRCs. We will hear from the center directors about their centers’ research vision for the future as they begin the next five years of effort. We are extremely pleased to welcome Dr. Katherine Yelick , the Associate Laboratory Director for Computing Sciences at Lawrence Berkeley National Laboratory. Dr. Yelick’s research is in high performance computing (HPC) research where she has worked on interdisciplinary teams developing scientific applications ranging from simulations of chemistry and fusion processes to phylogenetics and genome assembly. She currently leads one of DOE’s Exascale Computing Projects (ECP) entitled ‘Exabiome: Exascale Solutions for Microbiome Analysis,’ for developing scalable methods for metagenomic sequence assembly and analysis on HPC systems. This exciting new capability could have profound implications for microbiome research and we are confident Dr. Yelick’s presentation will be an excellent catalyst for scientific discussion throughout the meeting. This year researchers supported by the joint USDA-DOE Plant Feedstock Genomics for Bioenergy program will also be in attendance. Recent efforts in this area of the portfolio are targeting disease resistance in bioenergy feedstocks and genetic improvements to oilseed crops. A breakout session featuring 2016 and 2 2017 awardees will be held to discuss some of the very important developments in feedstock genomics research that have taken place since these groups last met, and to highlight the most recent awards. The KBase project will be hosting two afternoon sessions. The first will be a User Science session where current users will discuss science examples enabled by KBase capabilities. The second will be hands on experience for attendees to test the latest tools available in KBase in an interactive setting and discuss future capabilities with KBase staff. We also planned for a breakout session in Computational Biology that will feature new computational approaches for modelling and data analysis developed in various parts of the portfolio. In 2017, BSSD issued a Funding Opportunity Announcement for the next iteration of the Biosystems Design program element. This year’s meeting includes a breakout session featuring the twelve new Biosystems Design awards focused on the fundamental understanding needed to enable the design and engineering of plants and microbes for renewable production of biofuels and valuable chemicals. We hope these breakout sessions are informative and help to foster new collaborations across the portfolio. Finally, we are proud to once again host a plenary session featuring some of the most recent recipients of the Office of Science (SC) Early Career program awards. The Early Career program is one of the most competitive programs within SC and award recipients are part of an exclusive group. We are pleased to have four awardees present at this year’s meeting. Thank you again for making the program the success that it is. We look forward to an excellent meeting! Sincerely, Todd Anderson, Ph.D. Director, Biological Systems Science Division, SC-23.2 Office of Biological and Environmental Research Office of Science 3 Table of Contents (Click on Title to advance to the abstract) Madhu Khanna: Center for Advanced Bioenergy and Bioproducts Innovation: Sustainability Theme PRESENTER: Madhu Khanna Gerald Tuskan: Agile Technoeconomic and Life Cycle Assessments at the CBI PRESENTER: Mary Biddy Gerald Tuskan: Technoeconomic Analysis of Biofuel Feedstock Supplies to Inform Plant Development R&D PRESENTER: Erin Webb Corinne Scown: Simulating Near-Term Scale-Up of Cellulosic Biofuel Production Using Crop Residues and Biomass Sorghum PRESENTER: Xinguang Cui Andrew Vanloocke: Economic and Environmental Modeling of Bioenergy Production – Policy Impacts on Water Quality PRESENTER: Kelsie Ferin Eric Hegg: Progress Towards N2O Source Apportionment in Biofuel Soils: Understanding Sources of Variation in Isotopic Discrimination During Denitrification PRESENTER: Joshua Haslun Wendy Yang: Carbon Cycling in Biomass-Based Cropping Systems: Improving the Mechanistic Foundations of Plant, Microbial, and Soil Interactions PRESENTER: Adam von Haden Mary Firestone: Characterizing the Multitrophic Interactions that Mediate Carbon Flow in Soil PRESENTER: Javier Ceja-Navarro Thomas Bruns: Determination of the Roles of Pyrophilous Microbes in the Breakdown and Sequestration of Pyrolyzed Forms of SOM PRESENTER: Thea Whitman Daniel Buckley: Microbial contributions to carbon cycling differ qualitatively and quantitatively in agricultural, forest and meadow soils PRESENTER: Samuel Barnett Daniel Buckley: The Role of Surface-related Microbial Ecology in Organo-Mineral Stabilization of Carbon in Soil PRESENTER: Roland Wilhelm John Dunbar: Linking Genes to Ecosystem Processes: Microbial Nitrogen and Carbon Cycling PRESENTER: Michaeline Albright 4 Jillian Banfield: Microbial community proteogenomic analyses indicate extensive depth-dependent CO oxidation and C1 metabolism in soil and increased capacity for N2O reduction with increased rainfall PRESENTER: Spencer Diamond Kristen DeAngelis: The “Who” and “How” of Microbial Control over Soil Carbon Dynamics: a Multi – omics, Stable Isotope Probing, and Modeling Approach PRESENTER: Grace Pold Bruce Hungate: Understanding Soil Metabolism from Carbon Release and Carbon Incorporation from Position-Specific 13C-Labeled Substrates PRESENTER: Paul Dijkstra Jennifer Pett-Ridge: Redox Fluctuations Control Coupled Iron-Carbon Cycling and Microbial Community Structure in Tropical Soils PRESENTER: Amrita Bhattacharyya Virginia Rich: Modeling the Pathways to Carbon Liberation: Microbiologically-Informed C-Cycle Modeling in a Thawing Permafrost Landscape, for Scaling from Molecules to the Earth System PRESENTER: Eoin Brodie Virginia Rich: Subarctic Lake Sediment Microbial Community Contributions to Methane Emission Patterns PRESENTER: Joanne Emerson Kelly Wrighton: Methanogenesis in Oxygenated Soils is a Substantial Fraction of Wetland Methane Emissions PRESENTER: Kelly Wrighton Neslihan Tas: Understanding the microbial controls on biogeochemical cycles in permafrost ecosystems PRESENTER: Neslihan Tas Trent Northen: The importance of biocrust organics revealed by metabolite sorption studies and in situ imagery PRESENTER: Estelle Couradeau John Dunbar: Microbial Communities As Carbon Conductors: Elucidating Universal Traits Across Litter Types PRESENTER: Danielle Marias Jizhong