Expanding research communities and collaborations

October 29th, 2013
From the depths of ocean dead zones, to wide swaths of forests, and rising up to the troposphere, where most weather changes occur, the U.S. Department of Energy Joint Genome Institute (DOE JGI) 2014 Community Science Program portfolio seeks to parse functional information extracted from complex ecosystems to address urgent energy and environmental challenges. These massive, data-intensive undertakings require interdisciplinary approaches, many leveraging additional expertise through a new inter-DOE-Facility partnership.

Reflecting its vision of serving the scientific community as a next-generation genome science user facility, the DOE JGI has joined forces with the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory to provide complementary scientific resources to significantly expand genomic understanding to cellular function. The inaugural round of eight accepted proposals showcases the synergy between these two DOE user facilities.

Five of the eight new DOE JGI-EMSL proposals going forward will focus on carbon cycling and three relate to improvements in biofuels production. Each of these projects will tap the capabilities at both facilities to further the research in ways that would not otherwise be possible, and all are targeted for completion within an 18-month time window.

Two of the carbon cycling projects focus on soil microbial communities. Mary Firestone from the University of California, Berkeley will study the plant-soil-microbial interactions of an annual grass Avena fatua with soil from a California grassland, a model ecosystem for further exploration of the rhizosphere, the soil and microbial community around plant roots. By combining DNA sequencing with the study of unique chemical traces that the cells produce (metabolomics) and the large-scale study of their protein structures and functions (proteomics), this project will lend insights into how changing climate conditions might influence carbon cycling and carbon sequestration in terrestrial ecosystems. According to the U.S. Department of Agriculture, grasslands and rangelands account for approximately 50 percent of such areas and provide forage for livestock and native herbivores, habitat for native flora and fauna, watersheds for rural and urban uses, ecosystem goods and services, areas for recreation, and potentially for renewable and nonrenewable energy sources as well.

Kirsten Hofmockel from Iowa State University will combine the DOE JGI's high-throughput sequencing capabilities and EMSL's cell sorting technologies to conduct a large-scale comparative analysis of soil microbial communities. With an eye toward linking microbial community dynamics to ecosystem-scale biogeochemical models, the samples come from a study comparing four bioenergy cropping systems being conducted at Iowa State University's South Reynoldson Farm. Among the goals of this project is to develop novel labeling and cell sorting approaches to shed light on the structure and function of carbon cycling microbial communities within soil and to identify key soil carbon cycling organisms and their relationship with other community members and soil characteristics.

Another CSP 14 project, led by Marc Libault of the University of Oklahoma explores a single cell type model, the root hair cell, to advance our understanding of the response of soybean and sorghum plants to various environmental stresses.

Two other carbon cycling projects involve the study of cyanobacteria. Matthias Hess at Washington State University-Tri Cities will build off the DOE JGI's pioneering work in filling in gaps in the tree of life through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) pilot project and a recent spin-off focused specifically on cyanobacteria. The GEBA-Cyano project has doubled the amount and diversity of cyanobacterial genome sequence data in the public databases. Hess' project will develop a Functional Encyclopedia of Cyanobacteria with the help of samples provided by the Culture Collection of Microorganisms from Extreme Environments, to better understand photosynthetic microbial communities and their central role in carbon and nitrogen cycling. Another project comes from the J. Craig Venter Institute's Philip Weyman, who will study the interactions between the Pleurocarpous feathery moss and cyanobacteria found in boreal forests. Since these ecosystems are enormous carbon sinks, their health and productivity is of vital importance to monitoring and moderating future increases in CO2.

Another carbon cycling project involves a family of wood-degrading fungi known as Ascomycetes, which include molds and mildews. Colleen Hansel at the Woods Hole Oceanographic Institute will focus on these organisms, which take leading roles in breaking down lignocellulose in contaminated sites. The initial focus will be on sequencing samples that are isolated from contaminated freshwater lake sediments and coal mine drainage treatment systems, and then by using the metabolomic and proteomic analyses capabilities at EMSL she seeks to identify the metabolic pathways that are involved in breaking down carbon in these organisms.

Three projects focus on biofuels and the role of fungi improving production of them. Steve Harris from the University of Nebraska-Lincoln will build upon previous DOE JGI sequencing of the industrially important filamentous fungi Aspergillus niger and Trichoderma reesei. A strain of A. niger is critical to the large-scale production of citric acid while other strains provide enzymes that can break down plant cell walls to free up sugars that can then be fermented and distilled into biofuel. T. reesei is the workhorse organism for a number of industrial enzyme companies for the production of cellulases that can be used to break down plant biomass. The Harris team plans to harness genomic, proteomic, and microscopy data in order to facilitate the breeding of improved production strains for both fungi.

The proposal from Michelle O'Malley from the University of California, Santa Barbara also builds from a previous DOE JGI project, one that characterized the microbial communities in the cow rumen. In this new proposal, however, the researchers will target anaerobic fungi in communities isolated from large herbivores (elephant, giraffe, goat, horse, and sheep) that are involved in breaking down plant biomass. Novel isolates that possess desirable enzymatic properties will be used for the construction of metabolic models to drive improvements in bioprocessing strategies.

Finally, Harold Kistler from the U.S. Department of Agriculture-Agricultural Research Service will focus on compounds known as terpenoids that are produced by plants and filamentous fungi including Fusarium graminearum. The goal is to determine a way to efficiently and abundantly produce terpenoids in filamentous fungi, so that they can be evaluated as renewable biofuels that have higher energy content than ethanol and could be more compatible with existing fuel infrastructure. Aside from using the DOE JGI's RNA sequencing, the work will be enabled by EMSL's flow cytometry and mass spectrometry capabilities.

The remaining 29 accepted projects, more traditional DOE-JGI sequencing projects, were chosen for their relevance to other goals of the CSP 2014 call, and will be carried out entirely at DOE JGI. Farren Isaacs from Yale University is leading a DNA synthesis project that will identify and synthesize metagenome-derived enzymes that can be introduced into microbes to address challenges in bioremediation, global carbon cycling and development of alternative energy strategies. "Recent advances in synthetic biology increase the prospect of using engineered microorganisms for a myriad of these challenges," he noted in his proposal. "Developing genome engineering technologies to drive high-throughput genetic modifications across genomes of diverse microorganisms, would vastly expand our ability to utilize microorganisms for DOE mission objectives."

Another selected project will explore airborne microbial communities and their influences on the Earth's biogeochemical cycles. Kostas Konstantinidis from Georgia Tech and his colleagues are concentrating on airborne microbes in the upper trophosphere, a region that contains almost all the water vapor of the atmosphere. In particular, they are seeking to characterize the conditions enabling the survival of microbes in this layer and their roles in cloud formation and the water cycle. This linkage of microbial processes and climate change processes is a bold new direction for DOE JGI.

The DOE JGI Plant Flagship Genomes initiative is another area of emphasis for the 2014 CSP call. These are plants sequenced for their potential as feedstock crops for biofuel production or else as comparators that will assist in the interpretation of feedstock crop genomes and potentially lead to their improvement for purposes of biofuel development. Many of the six selected projects focus on the poplar (black cottonwood) tree—the first tree ever sequenced—and published by the DOE JGI in the journal Science back in 2006. For example, Jay Chen from Oak Ridge National Laboratory will investigate gene expression in poplar populations. The goal is to use the information to identify genetic elements and transcriptional networks involved in plant cell wall development to improve the development of poplar as a feedstock for cost-effective, sustainable biomass production and conversion into biofuels. Another project, from Jonathan Shaw of Duke University, will leverage the first moss genome sequenced – Physcomitrella patens - and expand the moss/bryophyte knowledgebase by sequencing peat moss (Sphagnum magellanicum) to learn more about its role on the global carbon budget.

Another area of interest in this year's CSP call is microbial diversity and function. Among the approved projects is one from Michael Wagner from Austria's University of Vienna, who will test a novel method for identifying ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in wastewater sludge. These bacteria are key drivers of the nitrogen cycle and essential in wastewater treatment plants for the removal of nitrogen from sewage.

A total of eight fungal projects were approved from this year's call. One is led by Istvan Molnar from the University of Arizona and focuses on gene clusters from sequences in the DOE JGI's fungal portal MycoCosm. The researchers will identify genes involved in producing compounds that play a role in plant-microbial interactions, plant stress tolerance or plant/fungal symbioses.

A third area of emphasis this year was microbial emission and capture of greenhouse gases in terrestrial systems. These projects focus on carbon capture, nitrogen processing and methane reduction. From the 10 prokaryotic projects approved out of the CSP 2014 call, many of them focus on understanding the roles of soil microbial communities on the carbon cycle in a number of environments. For example, Erik Lilleskov from the USDA Forest Service will study microbial communities involved in carbon cycle in peatland ecosystems. Peatlands, his proposal noted, represent up to five percent of the land surface but sequester as much as one third of the soil organic carbon.

The final area of emphasis for the call focused on the DOE JGI's DNA synthesis capabilities, and many of the six projects approved, including the one from Isaacs described earlier, primarily focus on exploring pathways that could lead to bioenergy and environmental applications. For example, the proposal from UC Berkeley's Ming Hammond will build and characterize a modular system for multi-gene regulation in plants. One application of this system is improving the cost-effective production of lignocellulosic biofuels as they focus on modifying gene expression to increase biomass density while reducing lignin—an integral part of the secondary plant cell wall, but a bottleneck to biofuels production.

All 37 projects selected by an external review panel out of 123 full proposals reflect the emphasis on collaboration between researchers and the potential of further expanding research communities working on these topics. Additionally, the projects selected combine sequence data generation with large-scale experimental and computational capabilities and the total allocation for the CSP 2014 portfolio is expected to be more than 30 trillion bases (terabases or Tb).

Together, all of these projects are the first selected under a new aegis as the DOE JGI's primary user program changes names from the Community Sequencing Program to the Community Science Program, a title that more accurately reflects the work being done by and at the DOE JGI. "The DOE JGI offers access to high throughput DNA sequencing, analysis of DNA sequence, and, recently, DNA synthesis for investigators who have questions of relevance to DOE mission areas," said Deputy Director of Programs Jim Bristow. The change, he added, aligns with the Institute's 10-year Strategic Vision to transition from a sequencing facility to a fully-fledged genomic analysis resource offering researchers the opportunity to submit a DNA sample of their organisms of interest and receive not just raw DNA sequence but detailed functional annotations that can be parlayed into a foundation for collaborative science.

Provided by DOE/Joint Genome Institute

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