Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment

Report from the September 2016 Workshop

The Biological Systems Science Division (BSSD) within the U.S. Department of Energy’s (DOE) Office of Biological and Environmental Research (BER) funds basic research on plants and microbes relevant to several DOE bioenergy and environmental mission areas. BSSD research seeks to understand the fundamental genome-encoded properties of plants and microbes that can be harnessed or redesigned for beneficial purposes.

Current emphases are leading to the discovery, development, and understanding of numerous plant and microbial species with traits suitable for the production of fuels and chemical products from renewable biomass that could be grown synergistically with food or animal feed crops while not competing with other societal needs. Additionally, BSSD further supports research leading to an understanding of the complex and essential interactions among plants, microbial communities, and the environment to find new ways to sustainably produce biomass for a range of bioenergy and bioproduct applications. This research also is relevant for incorporation into larger-scale environmental models such as those developed through the research supported by BER’s Earth and Environmental Systems Sciences program.

To engage the relevant scientific communities in discussions of these research areas, BER convened the Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment workshop on September 21–23, 2016. Seeking to enable more comprehensive systems biology–based approaches, which typically require measurements of many samples, workshop participants highlighted the need for the development of highly sensitive methods to provide accurate measurements from small sample volumes and that are operable in high-throughput or highly parallel modes.

Publication date: September 2017

Suggested citation for this report: U.S. DOE. 2017. Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment, DOE/SC-0189, U.S. Department of Energy Office of Science. (https://genomicscience.energy.gov/technologies/).

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Research Themes

These fundamental research efforts require new and innovative methods and technologies to elucidate the foundational principles that drive biological systems of interest to DOE’s energy and environmental missions. Characterizing biological systems involves analytical approaches that illuminate cellular components and their form, structure, size, function, spatial location, dynamics, and interactions with the environment. Workshop discussions identified new technologies and combinations of existing capabilities to address the challenges associated with characterizing molecular and cellular systems relevant to bioenergy and environmental research. Participants included technology developers and biology researchers with expertise in cellular ultrastructure and physiology, bioenergy and bioproducts, and environmental microbiology. Attendees developed a series of research and technology development needs across six thematic areas spanning the range of BSSD-supported research. The challenges of studying these systems are many and broad in scope, covering time scales from femtoseconds to weeks and length scales from Angstroms to centimeters. This report addresses this very broad measurement range—from cells and their metabolism and mineralogy (Angstroms to micrometers), to rhizosphere ecosystem processes and community biochemical activity (millimeters to a meter). In this context, the range from micrometers to a meter is referred to as “mesoscale.” Despite the breadth of the challenges, participants identified key needed technologies and improvements in current techniques that could advance BER science. These six major research themes are discussed below.

Cell Wall Composition and Degradation. The benefits from gaining a molecular-level understanding of plant cell wall composition and degradation were discussed in the context of using plants in the production of biofuels and bioproducts. As a renewable resource for biofuels and biomaterials, lignocellulosic biomass can partially replace the use of diminishing petroleum-based fuels and products and help meet increasing consumer demand for green chemicals. However, the varying structure and chemical composition of the cell walls of different plants and tissue types may hinder industrial-scale processes for converting biomass to bioproducts. Needed to address this challenge are better atomic- and molecular-level understandings of the structure and dynamics of naturally occurring cell wall processes, as well as the processes involved in the production of biofuels and other chemicals. Also needed are new characterization techniques with nanometer-scale resolution that require minimal sample preparation and keep the sample in close-to-natural conditions. Several technologies and techniques identified will aid the understanding of plant cell wall properties at the anatomical, cellular, molecular, and genetic levels. Other new approaches suggested will provide as-yet-undiscovered molecular details about structural and temporal rearrangement of cell wall components during biomass deconstruction prior to conversion to biofuels and bioproducts.
Rhizosphere Community Interactions. A better understanding of ecosystems is yielding deeper insights into plant-microbe-mineral interactions important for bioenergy production. Knowing the complex interdependencies of these three systems is critical to understanding and developing sustainable biofuel production practices. Root system architecture has a dramatic bearing on plant viability and crop productivity in given soil conditions. Namely, the rhizosphere, the area immediately surrounding plant roots, is a nexus of biological activity and the foundational ecosystem for any plant-microbe system. Thus, studies are needed of all essential communal elements necessary for plant growth and yield across a range of geographic regions. Understanding these ecosystems can enable the design of optimally mutualistic plant-microbe interactions to improve biofuel crop sustainability. For these studies, the development of penetrating imaging tools is needed to study entire, complex soil environments and root system architectures.
Biogeochemical Cycling. Environmental system function is intimately tied to the biogeochemical cycling of the major elements, particularly their reduction-oxidation (redox) transformations. Spatial and temporal imaging and measurements of biogeochemical systems are necessary for a mechanistic understanding of how different biogeochemical systems function. There also is a need for development of, and improvements to, technologies and approaches that will enable researchers (1) to understand and predict the dynamic interplay between environmental biotic and abiotic factors that often are opaque to imaging tools, from the molecular to the mesoscale, and (2) to use this new understanding to predict larger-scale phenomena. A combined and holistic use of a variety of dynamic imaging and characterization probes, coupled with multiomic and modeling approaches, is necessary to span spatial and temporal scales in biogeochemical systems to better understand their role in key environmental processes.
Metabolic Pathways in Plants, Microbes, and Fungi. Plants and microbes exchange metabolites in a community economy that ultimately determines the rates at which nutrients and water are extracted from soil and soil carbon is cycled (i.e., the biogeochemistry). A deeper understanding of the mechanisms by which organisms interact with each other in the environment, and the metabolic pathways and specific molecules involved in these interactions, will enable the modification of these pathways to improve nutrient-use efficiency and soil-carbon performance. New tools are required for predicting and measuring metabolites from organisms key to BER bioenergy and environmental missions. Combined with new higher-resolution approaches, these technologies will need capabilities for determining spatiotemporal localization and mechanisms responsible for metabolite synthesis, transport, degradation, and perception. The ultimate goal is a “balanced record” of metabolite economy among plant-microbe-fungi interactions and the environment that fully accounts for all carbon and nutrient cycling in the system.
Biosystems Design. Synthetic biology provides a valuable approach to probe, study, and engineer new functions into biological systems through the introduction or modification of metabolic pathways, specifically generating biologically derived chemicals, fuels, and materials to ensure environmental sustainability. Challenges include (1) applying synthetic biology to intractable eukaryotic and multicellular organisms, (2) engineering communities of microorganisms and microbe-plant interfaces, (3) exploring genotype-phenotype landscapes resulting from genome engineering, (4) isolating engineered organisms with desired functions, and (5) safeguarding engineered biosystems. Efficient tools for the precise manipulation of genomes in diverse target organisms will need to be combined with improved computational modeling methods to support predictive biology. These coupled approaches will require assistance from new methods for rapidly assaying function and fitness. They also must be applicable to technologies for controlling the containment of engineered systems and the products of engineered pathways.
Cellular Ultrastructure and Physiology. BER research examines a range of plant and microbial cell structures and organization, from the atomic level to complex molecular machines, cellular compartments, scaffolds, and whole cells. Workshop participants identified several measurement challenges, including how to detect and visualize cellular dynamic processes such as metabolic cycles, signaling and trafficking in plants, and interactions among microbial and fungal communities. They described needs for improved (1) structural imaging at the atomic and molecular level, (2) methods for illuminating whole organisms to understand the internal organization of cells, and (3) imaging chemical events that underlie biology. These needs include methods to determine the locations and dynamic parameters of enzyme reactions within cells, as well as the flow of chemicals and macromolecules within and between cells. The structural and dynamical insights from such studies will inform and enable more accurate modeling of biogeochemical cycling and metabolic pathways important in rhizospheric communities and biofuel or bioproduct processes.

Overarching Challenges and Opportunities

Spatial and Temporal Resolutions of Imaging Technologies. Summary of imaging and other selected measurement technologies discussed at the workshop. Mature technologies that will benefit from further development include X-ray and neutron crystallography and scattering, scanning probe microscopies, X-ray tomography, synchrotron spectroscopy, and confocal microscopy. Techniques undergoing rapid development and with potential application to the mission of the U.S. Department of Energy’s Office of Biological and Environmental Research (BER) include X-ray free-electron laser ultrafast diffraction, time-resolved X-ray scattering, cryo-electron microscopy (cryoEM) and cryo-electron tomography (cryoET), infrared imaging methods, super-resolution fluorescence imaging. New technologies not yet fully developed and applied to research supported by BER’s Biological Systems Science Division include dynamic EM, fluctuation scattering, ptychography, and in soil sensors. Key: Å, Angstrom; EXAFS, extended X-ray absorption fine structure; fs, femtosecond; ks, kilosecond; µm, micrometer; µs, microsecond; mm, millimeter; ms, millisecond; nm, nanometer; ns, nanosecond; ps, picosecond; s, second; SAXS, small-angle X-ray scattering; SEM, scanning electron microscopy; TEM, transmission electron microscopy; TIRF, total internal reflection fluorescence; USANS, ultrasmall-angle neutron scattering; WAXS, wide-angle X-ray scattering; XANES, X-ray absorption near edge structure.

Several challenges common to all the research themes emerged throughout workshop discussions. Translating information from genomic studies to the molecular and cellular realm for characterization will require increased throughput for existing technologies and the development of new high-throughput approaches. Achieving these goals will necessarily involve more automation and computational algorithms to manage the high data volumes that will be produced. Improved machine-learning approaches and large data-handling capacity will be essential. Integration of disparate data types from multiple and heterogeneous sources remains a challenge, so continued development of integrative and interpretive computational approaches is needed. Similar needs also were discussed at a workshop hosted by DOE’s Office of Advanced Scientific Computing Research (ASCR), the DOE Exascale Requirements Review, held March 28–31, 2016, in Rockville, Md., which generated the meeting report, ASCR Exascale Requirements Review

The tools and methods described in this BER report are critical for advancing the deep understanding of complex, multicomponent systems that are central to bioenergy and the environment. While new technologies are needed for advancing leading-edge biological insights, they are of limited value if they are not readily accessible by the scientists who need them to conduct their research. As new instruments, platforms, and approaches are created, it is important that they be developed in ways that ultimately enable biology researchers to use them, either by adopting them in their own laboratories or by having access to the tools, appropriate expertise, and support at national user facilities. Elements will include robust hardware, physiologically relevant sample preparation and measurement conditions, automation, sophisticated analytical algorithms, and user-friendly interfaces. For facility-based technologies, long-term and productive community access requires recognition of the need for ongoing operational support.

Described in the report are some of the workshop’s identified challenges to studying the biological systems of interest to BSSD, which has a history of developing and supporting highly sophisticated research tools and techniques and ensuring that researchers can access them to advance science in support of the division’s goals. Workshop discussions reflected in this document will help guide the next generation of imaging and analytical instrumentation needed to gain a predictive understanding of biological systems supporting DOE’s energy and environmental missions.