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We present draft genomes of two Paraburkholderia strains and two Burkholderia strains. Three strains were isolated from surrounding soils and one from roots of switchgrass (Panicum virgatum) in Michigan, USA.
Background: Members of the anaerobic thermophilic bacterial genus Caldicellulosiruptor are emerging candidates for consolidated bioprocessing (CBP) because they are capable of efficiently growing on biomass without conventional pretreatment. C. bescii produces primarily lactate, acetate and hydrogen as fermentation products, and while some Caldicellulosiruptor strains produce small amounts of ethanol C. bescii does not, making it an attractive background to examine the effects of metabolic engineering. The recent development of methods for genetic manipulation has set the stage for rational engineering of this genus for improved biofuel production. Here, we report the first targeted gene deletion, the gene encoding lactate dehydrogenase (ldh), for metabolic engineering of a member of this genus. Results: A deletion of the C. bescii L-lactate dehydrogenase gene (ldh) was constructed on a non-replicating plasmid and introduced into the C. bescii chromosome by marker replacement. The resulting strain failed to produce detectable levels of lactate from cellobiose and maltose, instead increasing production of acetate and H2 by 21-34% relative to the wild type and pyrFA parent strains. The same phenotype was observed on a real-world substrate switchgrass (Panicum virgatum). Furthermore, the ldh deletion strain grew to a higher maximum optical density than the wild type on maltose and cellobiose, consistent with the prediction that the mutant would gain additional ATP with increased acetate production. Conclusions: Deletion of ldh in C. bescii is the first use of recently developed genetic methods for metabolic engineering of these bacteria. This deletion resulted in a redirection of electron flow from production of lactate to acetate and hydrogen. New capabilities in metabolic engineering combined with intrinsic utilization of lignocellulosic materials position these organisms to provide a new paradigm for consolidated bioprocessing of fuels and other products from biomass.
Among themophilic consolidated bioprocessing (CBP) candidate organisms, environmental isolates of Clostridium clariflavum have demonstrated the ability to grow on xylan, and the genome of C. clariflavum DSM 19732 has revealed a number of mechanisms that foster solubilization of hemicellulose that are distinctive relative to the model cellulolytic thermophile Clostridium thermocellum. Growth experiments on xylan, xylooligosaccharides, and xylose reveal that C. clariflavum strains are able to completely break down xylan to xylose and that the environmental strain C. clariflavum sp. 4-2a is able to grow on monomeric xylose. C. clariflavum strains were able to utilize a larger proportion of unpretreated switchgrass, and solubilize a higher proportion of glucan, xylan, and arabinan, with strain 4-2a reaching the highest extent of solubilization of these components (64.7 to 69.4%) compared to C. thermocellum (29.5 to 42.5%). In addition, glycome immunoanalyses of residual plant biomass reveal differences in the extent of degradation of easily accessible xylans, with C. clariflavum strains having increased solubilization of this fraction of xylans relative to C. thermocellum. In conclusion, C. clariflavum strains exhibit higher activity than C. thermocellum in the breakdown of hemicellulose and are capable of degrading xylan to xylooligomers and xylose. This capability seems to also play a role in the higher levels of utilization of unpretreated plant material.
Data sets relating to the manuscript “Long-term yields in annual and perennial bioenergy crops in the Midwestern USA” published in Global Change Biology Bioenergy. Field data, including annual peak biomass and harvest yields from maize/soy, miscanthus, switchgrass, and prairie field trials from 2008-2018 are included. Peak and harvest biomass for fertilized and unfertilized miscanthus are included from 2014-2018.
Data sets for material included in "A 13-year record indicates differences in the duration and depth of soil carbon accrual among potential bioenergy crops" by Kantola et al., 2025, in Global Change Biology Bioenergy. Data include soil organic carbon (SOC), carbon stable isotope ratios, annual belowground biomass, and annual post-harvest litter for four crops, maize/soybean, miscanthus, switchgrass, and prairie, between 2008 and 2021.
The objectives of this study were to prepare a summary report that examines the opportunities for and obstacles to the integration of renewable energy resources in the Southeast between now and the year 2030. The report, which is based on a review of existing literature regarding renewable resources in the Southeast, includes the following renewable energy resources: wind, solar, hydro, geothermal, biomass, and tidal. The evaluation was conducted by the Oak Ridge National Laboratory for the Energy Foundation and is a subjective review with limited detailed analysis. However, the report offers a best estimate of the magnitude, time frame, and cost of deployment of renewable resources in the Southeast based upon the literature reviewed and reasonable engineering and economic estimates. For the purposes of this report, the Southeast is defined as the states of Alabama, Arkansas, Florida, Georgia, Kentucky, Louisiana, Mississippi, North Carolina, South Carolina, Tennessee, Virginia, and West Virginia. In addition, some aspects of the report (wind and geothermal) also consider the extended Southeast, which includes Maryland, Missouri, Oklahoma, and Texas. A description of the existing base of renewable electricity installations in the region is given for each technology considered. Where available, the possible barriers and other considerations regarding renewable energy resources are listed in terms of availability, investment and maintenance costs, reliability, installation requirements, policies, and energy market. As stated above, the report is a comprehensive review of renewable energy resources in the southeastern region of United States based on a literature study that included information obtained from the Southern Bio-Power wiki, sources from the Energy Foundation, sources available to ORNL, and sources found during the review. The report consists of an executive summary, this introductory chapter describing report objectives, a chapter on analysis methods and the status of renewable resources, chapters devoted to each identified renewable resource, and a brief summary chapter. Chapter 2 on analysis methods and status summarizes the benefits of integrating renewable energy resources in the Southeast. The utilization of the existing fuels, both the fossil fuels and the renewable energy resources, is evaluated. The financial rewards of renewable resources are listed, which includes the amount of fuel imported from outside the Southeast to find the net benefit of local renewable generation, and both the typical and new green job opportunities that arise from renewable generation in the Southeast. With the load growth in the Southeast, the growth of transmission and fossil fuel generation may not meet the growing demands for energy. The load growth is estimated, and the benefits of renewable resources for solving local growing energy demands are evaluated. Chapters 3-7 discuss the key renewable energy resources in the Southeast. Six resources available in this region that are discussed are (1) wind, including both onshore and offshore; (2) solar, including passive, photovoltaic, and concentrating; (3) biomass energy, including switchgrass, biomass co-firing, wood, woody biomass, wood industry by-products (harvesting residues, mill waste, etc.), agricultural byproducts, landfill gas to energy and anaerobic digester gas; (4) hydro; and (5) geothermal. Because of limited development, ocean wave and tidal were not considered to be available in significant quantity before 2030 and are not presented in the final analysis. Estimates on the location of potential megawatt generation from these renewable resources in the Southeast are made. Each chapter will describe the existing base of the renewable electricity installations in the region now and, when available, the base of the existing manufacturing capacity in the region for renewable energy resources hardware and software. The possible barriers and considerations for renewable energy resources are presented.
A conventional bale feedstock design has been established that represents supply system technologies, costs, and logistics that are achievable today for supplying herbaceous feedstocks as a blendstock with coal for energy production. Efforts are made to identify bottlenecks and optimize the efficiency and capacities of this supply system, within the constraints of existing local feedstock supplies, equipment, and permitting requirements. The feedstock supply system logistics operations encompass all of the activities necessary to move herbaceous biomass feedstock from the production location to the conversion reactor ready for blending and insertion. This supply system includes operations that are currently available such that costs and logistics are reasonable and reliable. The system modeled for this research project includes the uses of field-dried corn stover or switchgrass as a feedstock to annually supply an 800,000 DM ton conversion facility.
Some general themes in catalysis at LANL are: (1) Storage and release of energy within chemical bonds (e.g. H 2 storage in and release from covalent bonds, N 2 functionalization, CO 2 functionalization, H 2 oxidation/evolution, O 2 reduction/evolution); (2) Can we control the chemistry of reactive substrates to effect energy relevant transformations in non-traditional media (e.g. can we promote C-C couplings, dehydrations, or hydrogenations in water under relatively mild conditions)? (3) Can we supplant precious metal or rare earth catalysts to effect these transformations, by using earth abundant metals/elements instead? Can we use organocatalysis and circumvent the use of metals completely? (4) Can we improve upon existing rare earth catalyst systems (e.g. in rare earth oxides pertinent to fluid cracking or polymerization) and reduce amounts required for catalytic efficacy? Carbohydrates can be accessed from non-food based biomass sources such as woody residues and switchgrass. After extracted from the plant source, our goal is to upgrade these classes of molecules into useful fuels.
Our DOE funded project focused on characterizing natural variation in C4 perennial grasses including switchgrass (Panicum virgatum) and Hall’s panicgrass (Panicum hallii). The main theme of our project was to better understand traits linked with plant performance and that impact the utility of plant biomass as a biofuel feedstock. In addition, our project developed tools and resources for studying genetic variation in Panicum hallii. Our project successfully screened both Panicum virgatum and Panicum hallii diverse natural collections for a host of phenotypes, developed genetic mapping populations for both species, completed genetic mapping for biofuel related traits, and helped in the development of genomic resources of Panicum hallii. Together, these studies have improved our understanding of the role of genetic and environmental factors in impacting plant performance. This information, along with new tools, will help foster the improvement of perennial grasses for feedstock applications.
Growing switchgrass (Panicum virgatum L.) as an intercrop in managed loblolly pine (Pinus taeda L.) plantations has emerged as a potential source of bioenergy feedstock. Utilizing land resources between pine trees to produce an energy crop can potentially reduce the demand for land resources used to produce food; however, converting conventionally managed forest land to this new intercropping system constitutes changes in land use and associated management practices, which may affect the environmental and economic sustainability of the land. The overall objective of this project is to evaluate the environmental effects of large-scale forest bioenergy crop production and utilize these results to optimize cropping systems in a manner that protects the important ecosystem services provided by forests while contributing to the development of a sustainable and economically-viable biomass industry in the southeastern United States.
In response to the Energy Independence and Security Act (EISA), NETL conducted an LCA (LCA) of 10 fuel production pathways using Fischer-Tropsch synthesis. These pathways use varying combinations of coal and swithgrass feedstocks and two options for carbon management (sequestration or enhanced oil recovery). Only greenhouse gas (GHG) emissions are inventoried. Comparative analysis of the results demonstrate that higher percentages of biomass result in lower life cycle GHG emissions when using switchgrass. The choice of carbon management strategy has an effect on the results.
This project seeks to elucidate and harness the exceptional robustness of novel and undomesticated Y. lipolytica isolates, which were identified from a genetic diversity screening for compatibility with bioenergy development. Bioenergy-relevant isolates were further developed as microbial platforms for efficient conversion of undetoxified biomass hydrolysates into designer bio-esters continuously recovered by solvent extraction. The project has three major goals. Goal 1. Elucidate and enhance the endogenous metabolism of Y. lipolytica for superior growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates under hypoxic conditions. Goal 2. Understand and enhance the underlying mechanism of exceptional tolerance of Y. lipolytica to organic solvents. Goal 3. Elucidate and rewire endogenous metabolism of the most robust Y. lipolytica strains for effective conversion of accumulating lipids to designer bio-esters. Significant progress has been made toward completing all research goals. We elucidated and optimized the robustness of Y. lipolytica by utilizing mixed C5 and C6 sugars in switchgrass hydrolysates (SGH) for lipid production (Aim 1). We conducted extensive omics analysis to investigate how genetic diversity among Yarrowia strains, derived from natural isolates or developed through adaptive laboratory evolution, influences lipid production when utilizing SGH. In Aim 2, novel mechanisms and underlying genetics were discovered that enabled Yarrowia strains to thrive in cultures containing high ionic liquid (IL) concentrations. Amongst other novel findings, it was found that sterols strengthened cell membranes to confer IL toxicity resistance, specifically via increased ergosterol content upon exposure to IL. In Aim 3, mechanistic studies elucidated how Y. lipolytica utilized intracellular lipids and alkanes/alkenes, leading to our discovery of novel enzymes and pathways for making short-chain esters. Most notably, thermostable chloramphenicol transferases were repurposed to function as alcohol acetyltransferases in Y. lipolytica, as well as the Gram-negative and Gram-positive bacteria Escherichia coli and thermophile Clostridium thermocellum, respectively.
Phylogenetic tree of GAUT Protein Family and gene model, RNAi construct, and relative transcript abundance of GAUT4 in switchgrass, rice and poplar knockdown (KD) lines.
We analyzed phosphorus (P) inputs (fertilization and atmospheric deposition) and outputs (harvest and leaching losses) over seven years in three representative biomass crops—switchgrass ( Panicum virgatum L.), miscanthus ( Miscanthus X giganteus ) and hybrid poplar trees ( Populus nigra X P . maximowiczii ) – as well as in no-till corn (maize; Zea mays L.) for comparison, all planted on former cropland in SW Michigan, USA.
Tilletia maclaganii Tm001 NY21 genome; sample from smut-infected switchgrass cultivar 'Shawnee'
Sori from switchgrass rust infections of plants in nine locations were sequenced to a high depth using whole-genome sequencing, with the goal of determining genetic diversity and divergence across the pathogen's range.
Thermal, anaerobic environments rich in decaying plant material are a potential source of novel cellulolytic bacteria. Samples collected from geothermal aquifers in the Yellowstone National Park (YNP) were used to select for cellulolytic thermophiles. Laboratory enrichments on dilute-acid pretreated plant biomass (switchgrass, Populus), and crystalline cellulose (Avicel) resulted in the isolation of 247 environmental clones. The majority of individual clones were affiliated with the cellulolytic bacteria of phylum Firmicutes, followed by xylanolytic and saccharolytic members of the phylum Dictyoglomi. Among the Firmicutes, the clones were affiliated with the genera Caldicellulosiruptor (54.4%), Caloramator (11.5%), Thermoanaerobacter (8.8%), Thermovenabulum (4.1%), and Clostridium (2.0%). From established anaerobic thermophilic enrichments a total of 81 single strains of the genera Caldicellulosiruptor (57%) and Thermoanaerobacter (43%) were isolated. With continuous flow enrichment on Avicel, increases in the relative abundance of Caloramator sp. was observed over clones detected from the Caldicellulosiruptor. Complex communities of interacting microorganisms bring about cellulose decomposition in nature, therefore using up-to-date approaches may yield novel cellulolytic microorganisms with high activity and a rapid rate of biomass conversion to biofuels.
Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, biohydrogen production remains inefficient and heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium strain sapolanicus, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. sapolanicus ferments a variety of 5- and 6- carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen and acetate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.