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At least 145 records · Page 8

Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow ( Salix spp.)

Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid Salix purpurea, diploid Salix viminalis, and tetraploid Salix miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-resolution, Multi-scale Modeling for Scalable Macroalgae Production

Macroalgae harvested along coastlines and in the open ocean has traditionally been used as food for human consumption, animal feed, and fertilizer. The U.S. ARPA-E MARINER Program estimates that the nation has suitable conditions and geography to produce at least 500 million dry metric tons of macroalgae per year, yielding approximately 2.7 quadrillion BTUs of energy in the form of liquid fuel, which is roughly 10% of the nation’s annual transportation energy demand. Adverse environmental effects of nutrient overload and ocean acidification may also be reduced by large-scale macroalgae cultivation in many coastal ocean regions. However, the successful deployment of large-scale marine macroalgae farms for fuel production depends on ambient hydrodynamic conditions and nutrient availability, as well as their interactions with macroalgae farm structures. Pacific Northwest National Laboratory led an ARPA-E MARINER project to develop a set of numerical modeling tools capable of simulating ocean hydrodynamic and biogeochemical processes, macroalgae trajectories for free-floating systems, macroalgae growth and biomass yields, and hydrodynamic load on macroalgae canopies and farm structures using a multi-resolution and multi-scale approach. This set of modeling tools provides a suite of information essential for system design, optimal project siting, risk analysis, and management of macroalgae production systems in the ocean. Better clarity can also help macroalgae system developers reduce deployment costs, operational risk, and potential impacts on the local marine environment.

59 BASIC BIOLOGICAL SCIENCES↗

Life Cycle Emissions and Health Cost Impacts of Producing Ethanol and Electricity from Willow and Switchgrass in the Riparian Buffers of Mid-Atlantic United States

The United States (US Mid-Atlantic Region (MAR) has the potential to grow a variety of perennial feedstocks such as switchgrass and shrub willow to increase domestic energy production. These cellulosic feedstocks have also shown improved ecosystem services, such as soil carbon sequestration, nitrate leaching reduction, and flood mitigation along rivers and streams as partially harvested riparian buffers. To examine the effects on greenhouse gases (GHGs) and criteria air pollutants (CAPs) from using these feedstocks to produce ethanol or electricity, we conducted a comprehensive life cycle assessment (LCA) and estimated the impact on human health costs when land use is changed from corn production for ethanol. Results indicate up to 54% reduced GHG per hectare from using willow and switchgrass feedstock sources to produce ethanol instead of corn. However, there was a trade-off in terms of CAP emission, as grass-based energy emitted more NO x and SO x compared to the corn ethanol pathway, except for SO X emissions from willow-based electricity. Electricity from cellulosic biomass had higher particulate matter (PM) emission compared to that from corn ethanol. Estimates for health cost to society ranged from $2498 ha –1 for electricity from switchgrass to a net benefit of $448 ha –1 for ethanol production from willow, depending on varying biomass yield under different market scenarios. Although using cellulosic feedstocks to produce bioenergy has great potential to reduce GHG emissions, CAP control measures are needed to manage CAP-induced health costs.

Bioenergy↗

BETO 2021 Peer Review - Improving Formate Upgrading by Cupriavidus Necator 2.3.2.111

Formate can be generated by electrocatalytic reduction of CO2 and has been proposed as a soluble intermediate for the storage of carbon and energy. Biological systems capable of assimilating formate could enable conversion of formate generated from low-cost renewable energy and waste CO2 to myriad fuels and chemicals. To that end, the goal of this project is to develop the natural formatotroph Cupriavidus necator as a robust microbial chassis for efficient conversion of formate to value-added products. Using a combination of laboratory evolution and rational engineering, we have identified mutations and genetic deletions that improve its growth rate and biomass yield on formate by 1.2X. Using RNA-seq transcriptomics, we are elucidating the mechanisms that underly these improvements and anticipate this will contribute to our understanding of formate conversion. We have also engineered C. necator to convert formate to the potential polymer precursor 2-hydroxymuconate semialdehyde (2HMS) by introducing an exogenous pathway and deleting competing pathways and demonstrated production and robust growth using a pH-stat bioreactor. Final techno-economic analysis and life-cycle assessment on biological production of 2HMS from formate will enable the DOE and other stake holders to evaluate the economic and environmental impact of this project and related technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Global Life Cycle and Techno-Economic Assessment of Algal-Based Biofuels

Techno-economic analyses (TEAs) and life cycle assessments (LCAs) of algal biofuels often focus on locations in suboptimal latitudes for algal cultivation, which can under-represent the sustainability potential of the technology. This study identifies the optimal global productivity potential, environmental impacts, and economic viability of algal biofuels by using validated biophysical and sustainability modeling. The biophysical model simulates growth rates of Scenedesmus obliquusbased on temperature, photoinhibition, and respiration effects at 6685 global locations. Region-specific labor costs, construction factors, and tax rates allow for spatially resolved TEA, while the LCA includes regional impacts of electricity, hydrogen, and nutrient markets across ten environmental categories. The analysis identifies optimal locations for algal biofuel production in terms of environmental impacts and economic viability which are shown to follow biomass yields. Modeling results highlight the global variability of productivity with maximum yields ranging between 24.8 and 27.5 g m -2 d -1 in equatorial regions. Environmental impact results show favorable locations tracked with low-carbon electricity grids, with the well-to-wheels global warming potential (GWP) ranging from 31 to 45 g CO 2eq MJ -1 in South America and Central Africa. When including direct land use change impacts, the GWP ranged between 44 and 55 g CO 2eq MJ -1 in these high-productivity regions. Low-carbon electricity also favors air quality and eutrophication impacts. The TEA shows that minimum algal fuel prices of $\$1.89$-$\$2.15$ per liter of gasoline-equivalent are possible in southeast Asia and Venezuela. Furthermore, this discussion focuses on the challenges and opportunities to reduce fuel prices and the environmental impacts of algal biofuels in various global regions.

09 BIOMASS FUELS↗

Integrated Pest Management (IPM) for Early Detection Algal Crop Protection. Final Report

During large-scale, outdoor algal biomass growth, production strain(s) are subject to attack by pathogens, predators, and non-productive competitors, compromising the biomass yield. The project team at UCSD developed and demonstrated the effectiveness of Volatile Organic Compound, VOC, analysis via mass spectrometry (MS) as an early detection system for the presence of production algal ponds infection. The MS detection can then trigger high-resolution melt analysis (HRMA) and enhanced quantitative PCR (qPCR) to identify predatory or pathogenic species precisely. This study gathered the foundational data informing how wholly automated systems monitor the health of production ponds. By detecting the presence of low molecular weight VOCs in the air space above ponds, the instrument was able to mimic “sniffing” the health of the algae pond. This early warning system will be free growers from time-consuming and costly regular surveillance of ponds with the current techniques, such as qPCR and flow-cam assays, which are slower, less sensitive, and not easily fully automated, resulting in increased production efficiency through the reduction of crop loss. This project demonstrated that Chemical Ionization Mass Spectrometry, CIMS, could serve as a real-time monitor of ponds health tracking up to 100 different VOCs simultaneously for continuous periods up to 60 days without interruption, signaling infection within an algal crop 24 to 36 hours prior to techniques such as qPCR and microscopy. While mass spectrometry is an expensive tool, this simple VOC sampling system proved not only to be sensitive and robust but could to multiplexed to monitor several ponds, lowering the overall cost serially. This technology demonstrated a reduction in biomass production cost by approximately 50% compared to growers not employing any detection methodology.

09 BIOMASS FUELS↗

A data base of crop nutrient use, water use, and carbon dioxide exchange in a 2O square meter growth chamber: I. Wheat as a case study

A data set is given describing the daily nutrient uptake, gas exchange, environmental conditions, and carbon (C), and nutrient partitioning at harvest for the entire canopy and root system of a wheat crop (Triticum aestivum, cv. Yecora Rojo). The data were obtained from a 20 m2 stand of wheat plants grown from planting to maturity in a closed, controlled environment, and include daily nutrient uptake [macronutrients, nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S); and micronutrients, iron (Fe), boron (B), manganese (Mn), zinc (Zn), copper (Cu), and molybdenum (Mo)], canopy carbon dioxide (CO2) exchange rates, and transpiration. Environmental factors such as relative humidity, air temperature, nutrient solution temperature, pH and electrical conductivity, and photoperiod were controlled in the chamber to specific set points. A detailed description of biomass yield for each of the 64 plant growth trays comprising the 20 m2 of growth area is also provided, and includes dry weights of grain, straw, chaff, and roots, along with the concentration of nutrients in different plant tissues and the percent carbohydrate, fat, and protein. To our knowledge, this information represents one of the most extensive data sets available for a canopy of wheat grown from seed to maturity under controlled environmental and nutritional conditions, and thus may provide useful information for model development and validation. A methods section is included to qualify any assumptions that might be required for the use of the data in plant growth models, along with a daily event calendar indicating when adjustments in set points and occasional equipment or sensor failures occurred.

NASA Discipline Number 61-20↗

Data for Application of Time-Domain 1H NMR for Investigating Dynamics of Vegetative Lipids in Bioenergy Crops at Different Developmental Stages

Sweet sorghum is typically cultivated for the food and fodder market. Recently, sweet sorghum varieties are being metabolically transitioned to enhance energy density by accumulating oil droplets in their vegetative tissues for bioenergy applications. Owing to the high biomass yield of sorghum, the transgenic lines can compete with oil-seed crops for biodiesel yield per unit area. In the initial phase of transgenic development, a high-throughput phenotyping method can bridge the gap between the production pipeline and analysis to improve the efficiency of the process. To meet the requirement, the present study extends the application of time-domain 1H-NMR spectroscopy for rapid quantification and characterization of the total in-situ lipids of sweet sorghum ‘ramada’ to lay the groundwork for analyzing the upcoming large quantity of transgenic samples. NMR technology has been successfully established for analyzing lipid contents of vegetative tissues of non-transgenic variety. The multiexponential analysis of spin-lattice (T1) relaxation spectra obtained from TD-NMR aided the investigation of the dynamics of the free and bound lipid fraction with plant development. The total lipid concentration of bagasse and leaves of non-transgenic sweet sorghum remained unchanged throughout the plant development. Leaves displayed a higher percentage of bound lipids as compared to bagasse. A significant variation in the lipid concentration of juice was observed at the different growth stages with a maximum lipid accumulation of 1.21 ± 0.04% w/w at the boot stage that decreased with further maturity of the plant.

Biomass Analytics↗

IX Cell Wall Research Conference 2022 (IXCWRC): Cell wall research for new fundamental discoveries and applications in plant biology

This application is for securing funds to offset the registration fees and lodging costs for US-based early career investigators (ERCs) to participate to the IX Cell Wall Research Conference 2022 (IXCWRC 2022): Cell wall research for new fundamental discoveries and applications in plant biology. The conference will be held in East Lansing, Michigan on June 13-17, 2022. The conference will focus on the plant cell wall. Plant cells are encapsulated by the cell wall, a dynamic structure that protects them, enables them to interface with the external environment and supports the growth of the entire organism. There is a growing interest in understanding the complex processes necessary to build and deconstruct the plant cell wall. A better understanding of how the cell wall is synthesized during plant growth and in response to the environment, and how it is deconstructed for a broad variety of applications can inform and improve biotechnological processes for increasing biomass yield and improving industrial processes for the recovery of valuable, sustainable polymers. Acquiring such knowledge requires the exchange of new ideas and results as well as the development and application of new technologies. The IXCWRC 2022 aims to reach this goal by providing an opportunity for an open forum to discuss new ideas and theories and develop collaborations for scientists across the globe in a diverse and supportive environment. A distinction of the IXCWRC 2022 from all the preceding plant cell wall conferences will be its focus on the training and inclusion of the next generation of scientists, the ERCs. The overall goal of this application is to broaden the participation of ERCs with a focus on underrepresented communities. The specific goal of this application is to secure support for registration and lodging for US-based ERCs to attend the conference. Priority will be given to ERCs from underrepresented communities in science. We expect that support from DOE will allow the development of an exciting and innovative program to discuss the latest scientific advances in cell wall biology research, advance the next generation of plant cell wall researchers and foster the foundations of an inclusive community in science.

59 BASIC BIOLOGICAL SCIENCES↗

Multifunctional landscapes for dedicated bioenergy crops lead to low-carbon market-competitive biofuels

Switchgrass is a promising feedstock for cellulosic biorefineries, due to its ability to maintain comparatively high biomass yields across a wide range of soil and climatic conditions. However, there is an incomplete understanding of the economic and environmental tradeoffs associated with cultivating switchgrass on low-productivity land for conversion to biofuels. This study surveys prior literature and demonstrates a new integrated assessment framework, including agroecosystem, ecosystem services valuation, technoeconomic, and life-cycle assessment models, to quantify and contextualize the economic and environmental impacts of switchgrass cultivation on marginal land with downstream conversion to biofuels. Monetizing and incorporating the value of ecosystem services, such as improved water quality benefits from nitrate and sediment reductions, climate change mitigation benefits from CO 2 emission reduction, and recreational and pollination benefits from increased biodiversity, the modeled multifunctional landscape reduces the ethanol production cost by 33.3–58.9 cents/$\scriptsize{L}$-gasoline-equivalent ($\$$1.3–2.2/gge). Planting switchgrass in low productivity land improves soil health, resulting in the carbon footprint reduction credit of 12.8–20.2 gCO 2e /MJ. For an improved switchgrass-to-ethanol conversion pathway with the maximum benefits from ecosystem services, the minimum ethanol selling price and carbon footprint of ethanol, respectively, could reach to 31 cents/$\scriptsize{L}$-gasoline-equivalent (47% reduction relative to average gasoline price) and 3 gCO 2e /MJ (97% reduction relative to gasoline). In conclusion, this low carbon renewable ethanol leads to substantial State and/or Federal policy incentives (~$\$$1/$\scriptsize{L}$-gasoline-equivalent) providing a large benefit to biorefinery operators, farmers, and the public as a whole.

09 BIOMASS FUELS↗

Simultaneous Overexpression of FERULOYL‐CoA 6′‐HYDROXYLASE 1 and COUMARIN SYNTHASE Leads to Coumarin‐Enriched Lignin and Improved Saccharification in Greenhouse‐ and Field‐Grown Poplar

ABSTRACT The urgent need for renewable resources has increased the interest in woody biomass to manufacture bio‐based products. However, lignin recalcitrance limits the enzymatic conversion of wood into fermentable sugars, posing a major challenge for biomass deconstruction. To address this problem, we aimed at incorporating the coumarin scopoletin into the lignin polymer of poplar ( Populus tremula × P . alba ) by expressing FERULOYL‐CoA 6′‐HYDROXYLASE 1 ( F6′H1 ) and COUMARIN SYNTHASE ( COSY ) in lignifying cells. Three constructs were evaluated: two bicistronic constructs, SCOP1 ( COSY followed by F6′H1 ) and SCOP2 ( F6′H1 followed by COSY ), and one monocistronic, SCOP3 (only F6′H1 ). SCOP1 poplars produced most free scopoletin without altering overall lignin, cellulose or hemicellulose content. SCOP2 poplars were overall less efficient in scopoletin production and most of these lines showed a severe biomass yield penalty, whereas SCOP3 caused plant lethality. NMR and metabolic analyses confirmed that scopoletin cross‐coupled with G and S monomers during lignification in SCOP1 lines. In addition to scopoletin, the detection of benzodioxane structures revealed the incorporation of dihydroxycoumarins. Overall coumarin incorporation in lignin amounted up to 2.3%. After alkaline pretreatment, wood from greenhouse‐grown SCOP1 poplars released up to 29% more glucose compared to the wild type upon limited saccharification. Field‐testing of three SCOP1 lines showed a 6 to 11% increase in saccharification efficiency, with the line containing the lowest scopoletin levels maintaining normal growth. These results demonstrate that engineering lignin composition in poplar can improve saccharification, and emphasize the importance of construct design, translational research and field validation.

alternative lignin monomers↗

Microbial maintenance energy quantified and modeled with microcalorimetry

Refining the energetic costs of cellular maintenance is essential for predicting microbial growth and survival in the environment. In this work, we evaluate a simple batch culture method to quantify energy partitioning between growth and maintenance using microcalorimetry and thermodynamic modeling. The constants derived from the batch culture system were comparable to those that have been reported from meta-analyses of data derived from chemostat studies. The model accurately predicted temperature-dependent biomass yield and the upper temperature limit of growth for Desulfovibrio alaskensis G20, suggesting the method may have broad application. An Arrhenius temperature dependence for the specific energy consumption rate, inferred from substrate consumption and heat evolution, was observed over the entire viable temperature range. By combining this relationship for specific energy consumption rates and observed specific growth rates, the model describes an increase in nongrowth associated maintenance at higher temperatures and the corresponding decrease in energy available for growth. This analytical and thermodynamic formulation suggests that simply monitoring heat evolution in batch culture could be a useful complement to the recognized limitations of estimating maintenance using extrapolation to zero growth in chemostats.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancing Biomass Productivity by Forecast‐Informed Pond Operations

ABSTRACT Microalgal cultivation for biofuels and proteins holds significant promise but faces challenges in achieving economically viable biomass productivity under variable environmental conditions. This study introduces a forecast‐informed pond operation (FIPO) system that uses numerical weather prediction (NWP) ensemble forecasts and the biomass assessment tool (BAT) to optimize daily dilution rates for enhanced biomass production. In contrast to the current practice, where fixed dilution rates are based on operator experience, the FIPO system determines the optimal dilution rate based on future weather forecasts and biomass growth conditions. Our experiments validate the effectiveness of FIPO in both short‐ and long‐term growth scenarios. In short‐term experiments, FIPO increased biomass production by 21.3% compared to batch growth and 7.4% over fixed dilution (60% every 3 days) operations. The NWP forecast‐informed operations achieved biomass production nearly identical to that using perfect weather forecasts, highlighting the accuracy of current NWP forecasts for guiding pond operations. In long‐term experiments, FIPO resulted in biomass production increases of 13.3% and 17.8% compared to two fixed dilution rates (60% every 3 days and 20% daily). These findings underscore the viability of using NWP forecasts to optimize microalgal cultivation systems. By adjusting daily dilution rates in response to forecasted weather, operators can achieve higher biomass yields and mitigate risks associated with environmental variability. This study provides a foundation for future research and practical applications in commercial‐scale microalgal production.

Yan, Hongxiang [Energy and Environment Directorate↗

The genetic architecture of biomechanical traits in sorghum

Sorghum bicolor (L.) Moench is the fifth most commonly grown cereal crop worldwide with unrivaled drought tolerance compared with other cereal crops. Drought and heat tolerance and high biomass yield potential make sorghum a promising bioenergy crop. However, stem lodging is a significant problem that results in substantial yield losses. Stem biomechanical traits influence the mechanical stability of crops and breeding for desirable biomechanical traits may result in improved lodging resistance. In this study, we report the identification of quantitative trait loci (QTL) for stem mechanical and morphological traits in three recombinant inbred line (RIL; populations from Tx623/Rio, Tx623/Della, and Tx631/Della) crosses between elite grain and sweet sorghum parents. The genetic architecture of stem biomechanical traits in the three RIL populations is multigenic and pleiotropic. Additionally, eight QTL affecting mechanical and morphological traits were detected; two main effects of these QTL were consistently found in all populations and colocated with previously identified dwarfing genes Dw1 and Dw3. These results indicate that dwarfing genes affect the mechanical properties of sorghum stems and their lodging resistance, while also having demonstrable effects on stem morphology. The identification of these QTL provides new opportunities for improving stem lodging resistance via genomics-assisted breeding.

59 BASIC BIOLOGICAL SCIENCES↗

Long-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analyses

Nitrogen (N) fertilizer has often been generously applied to increase crop biomass yield. Although the influences of inorganic N fertilizer on soil microbial communities have been widely studied, the effect of N fertilizer on microbial co-occurrence networks and its metagenome is largely unknown. Further, seasonal changes in microbial community responses to N addition have rarely been reported. In this study, three N fertilizer rates (0, 56, 196 kg N/ha) were applied annually in switchgrass (Panicum virgatum L.) grown for bioenergy production in the upper Midwest, USA. The soil microbiome was affected by both fertilizer and low pH in the 7th year of fertilization treatments. The microbial community structures were relatively stable during the growing season for each N fertilizer rate. However, the excess N fertilizer (196N) increased the seasonal variation of bacterial and fungal communities. Network analysis showed that the microbial interactions at the 196N treatment were more intense, with decreased bacteria-fungal interactions compared to 56N and 0N. Furthermore, this suggests that the microbial community became more sensitive to environmental change under the influence of long-term excess N fertilizer. Metagenomic analysis showed that the long-term excess N fertilizer promoted many metabolic processes, especially carbohydrate and amino acid related metabolism and Archaea mediated ammonia oxidation. However, N fertilizer also reduced many other traits, especially N 2 fixation and signal transduction, the latter of which may contribute to the decreased interactions between bacteria and fungi.

54 ENVIRONMENTAL SCIENCES↗

Microbe of the month: Methanococcus maripaludis

Methanococcus maripaludis was first isolated in 1983 from the anoxic sediment of a salt marsh in South Carolina, USA. M. maripaludis grows by using H 2 or formate to reduce CO 2 to CH 4 and is an autotroph that assimilates CO 2 via the archaeal version of the Wood–Ljungdahl pathway. In some strains, supplementation of growth medium with acetate or propionate can increase biomass yield. Furthermore, this microorganism is strictly anaerobic, has a pleomorphic coccoid shape, and forms translucent, pale yellow, smooth colonies within 3 days on agar plates. The optimum temperature for growth is 38°C with optimal pH between 6.8 and 7.2.

59 BASIC BIOLOGICAL SCIENCES↗

Quantifying the propagation of parametric uncertainty on flux balance analysis

Flux balance analysis (FBA) and associated techniques operating on stoichiometric genome-scale metabolic models play a central role in quantifying metabolic flows and constraining feasible phenotypes. At the heart of these methods lie two important assumptions: (i) the biomass precursors and energy requirements neither change in response to growth conditions nor environmental/genetic perturbations, and (ii) metabolite production and consumption rates are equal at all times (i.e., steady-state). Despite the stringency of these two assumptions, FBA has been shown to be surprisingly robust at predicting cellular phenotypes. In this paper, we formally assess the impact of these two assumptions on FBA results by quantifying how uncertainty in biomass reaction coefficients, and departures from steady-state due to temporal fluctuations could propagate to FBA results. In the first case, conditional sampling of parameter space is required to re-weigh the biomass reaction so as the molecular weight remains equal to 1 g mmol –1 , and in the second case, metabolite (and elemental) pool conservation must be imposed under temporally varying conditions. Results confirm the importance of enforcing the aforementioned constraints and explain the robustness of FBA biomass yield predictions.

59 BASIC BIOLOGICAL SCIENCES↗