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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Phylogenomic discovery and engineering of nitrogen fixation into the bioenergy woody crop poplar

Biological nitrogen fixation (BNF) is a key process enabling plants in specific lineages to convert atmospheric dinitrogen (N₂) into bioavailable ammonia through symbioses with diazotrophic microbes. Expanding this capability beyond native nitrogen-fixing clades into non-nodulating crops would reduce synthetic fertilizer use, lowering energy inputs and environmental impacts in agriculture. Supported by DOE Funding Award DE-SC0018247, the NitFix project advanced foundational knowledge required to engineer root-nodule symbioses in new host species. The team generated the most comprehensive phylogenomic analysis to date of all known nodulating lineages, resolving the evolutionary history of nitrogen-fixing symbiosis and identifying core gene suites retained across nodulating taxa. Through multimodal genomics, transcriptomics, and functional analyses in Medicago truncatula and related species, the project mapped regulatory networks underlying nodule organogenesis, bacterial infection, and nitrogen-fixation efficiency. Key discoveries include the identification of conserved signaling modules for rhizobial recognition, transcription factors controlling nodule differentiation, and metabolic pathways integrating fixed nitrogen into plant growth. The project also developed enabling tools—including optimized transformation pipelines, gene-editing workflows, and imaging-based phenotyping—to accelerate engineering efforts in emerging models. Together, these results refine the mechanistic framework of symbiotic nitrogen fixation and highlight transferable components essential for rewiring these traits into non-nodulating crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Generating Co-expression Networks for Three Cyanobacteria: Synechococcus sp. PCC 7942, Synechococcus sp. PCC 7002, Synechocystis sp. PCC 6803

Cyanobacteria are photosynthetic organisms capable of high growth rate and represent a promising bioplatform for harnessing the sun’s energy to make biofuel. Additionally, the process of photosynthesis absorbs CO2 from the environment. Understanding the metabolic processes involved in photosynthesis could lead to solutions to the recent rise of CO2 concentration in Earth’s atmosphere and the associated climate change. More research on the transcriptional regulation of these cells is needed to learn how to harness the untapped potential of cyanobacteria for these applications. Transcriptional analysis via RNA-seq provides an understanding of how gene expression changes at the mRNA level under diverse growing conditions. I systematically collected and analyzed RNA-Seq data obtained under a variety of conditions and available on the NCBI database for three cyanobacteria model organisms: Synechococcus elongatus sp. PCC 7942, Synechococcus sp. PCC 7002, and Synechocystis sp. PCC 6803. For each organism, the data was mapped to a reference genome to characterize the RNA expression profile. Samples were checked for quality based on the number of reads and the correlation of the expression profile between labeled replicates. All samples were transformed into transcripts per million reads, followed by a log transformation to account for the wide range of sample sizes. Gene co-expression networks were generated and analyzed for each species using Cytoscape. These networks provide a base level of gene expression for each species. The network topology and high-betweeness nodes of these networks need to be analyzed further to provide insight on potential ways to harness cyanobacteria genetics. Additionally, these datasets can be used together to form a core genome network analysis- one that includes only the genes that are homologous between the three species. This project has prepared the way for a more in-depth study on photosynthetic microbes on a genetic level.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2019

Synthesis of Meteoritic Reaction Intermediates

The organic compounds of carbo- naceous chondrites are structurally diverse products of the prolonged abiotic chemistry that occurred before and during the early stages of the solar system [1]. They also represent the types of prebiotic compounds that may have participated in chemical evolutionary processes that gave rise to life [2]. Pyruvic acid is a key component of primary metabolism that has recently been found in carbonaceous chondrites [3]. Its prominence in biology has inspired us to explore its chemistry and possible role in the origin of metabolism. Our laboratory investigations have found that pyruvate (the ionized form of pyruvic acid) can serve as a single-source reactant to generate what we term a pyruvate reaction network (PRN). The core of the PRN is driven by pyruvate aldol polymerization and decay reactions. These decay reactions lead to the production of stable and unstable compounds which include mono, di, and tricarboxylic acids and a variety of keto acids. Finding evidence of this reaction network in meteorites would establish that the chemistry of pyruvate did occur in a prebiotic environment. Many of the known compounds found in pyruvate reaction mixtures were originally detected in meteorite samples by Cooper et al in 2011. However, multiple synthetic origins not tied to pyruvate chemistry might also explain their meteoritic presence. Thus, a search to find compounds unique to the PRN, such as reaction intermediates, would provide stronger evidence to demonstrate its prebiotic relevance. The identity of these intermediates can only be confirmed by acquiring chemical standards, however, as most are not available commercially, they need to be accessed through chemical synthesis.

Rios, Andro C.↗
DOE OSTI2023

Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model

Graphene oxide (GO) nanomaterials have unique physicochemical properties that make them highly promising for biomedical, environmental, and agricultural applications. Despite the increasing interest and the use of GO, assessments of its nanotoxicity have largely not interrogated its potential impact on the gut microbiome. This study addresses an important knowledge gap by investigating the impact of GO exposure- both at low (25 ppm) and high (250ppm) doses and fed (nutrient rich) and fasted (nutrient deplete) conditions- on the gut microbial community structure and function, using an in vitro human colon bioreactor model. 16S rRNA amplicon sequencing revealed that GO exposure resulted in a restructuring of community composition. 25 ppm GO induced a marked decrease in the Bacteroidota phylum and increased the ratio of Firmicutes to Bacteroidota (F/B). Untargeted metabolomics on the supernatants indicated that 25 ppm GO impaired microbial utilization and metabolism of substrates (amino acids, carbohydrate metabolites) and reduced production of beneficial microbial metabolites such as 5-hydroxyindole-3-acetic acid and GABA. Exposure to 250 ppm GO resulted in community composition and metabolome profiles that were very similar to the controls that lacked both GO and digestive enzymes, suggesting that high concentrations of GO may interact with digestive enzymes to form protein coronas, causing their depletion in the gut environment. Differential abundance analyses revealed that 3 genera from the phylum Bacteroidota (Bacteroides, Dysgonomonas, and Parabacteroides) were more abundant after 250 ppm GO exposure, irrespective of feed state. Integrative correlation network analysis indicated that the phylum Bacteroidota showed strong positive correlations to multiple microbial metabolites including GABA and 3-indoleacetic acid, are much larger number of correlations compared to other phyla. These results show that GO exposure has a significant impact on gut microbial community composition and metabolism and different mechanisms are at play for low and high GO concentrations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mitochondrial integration and ovarian cancer chemotherapy resistance

Ovarian cancer has been nicknamed the “silent killer”. Most patients with ovarian cancer are diagnosed at an advanced stage of the disease for the first time because of its insignificant early clinical symptoms. In addition to the difficulty of early screening and delay in diagnosis, the high recurrence rate and relapsed refractory status of patients with ovarian cancer are also important factors for their high mortality. Patients with recurrent ovarian cancer often use neoadjuvant chemotherapy followed by surgery as the first choice. However, this is often accompanied by chemotherapy resistance, leading to treatment failure and a mortality rate of more than 90%. In the past, it was believed that the anti-tumor effect of chemotherapeutics represented by cisplatin was entirely attributable to its irreversible damage to DNA, but current research has found that it can inhibit cell growth and cytotoxicity via nuclear and cytoplasmic coordinated integration. As an important hub and integration platform for intracellular signal communication, mitochondria are responsible for multiple key factors during tumor occurrence and development, such as metabolic reprogramming, acquisition of metastatic ability, and chemotherapy drug response. The role of mitochondria in ovarian cancer chemotherapy resistance is becoming increasingly recognized. In this review, we discuss the cellular interactive regulatory network surrounding mitochondria, elucidate the mechanisms of tumor cell survival under chemotherapy, and discuss potential means of interfering with mitochondrial function as a novel anti-cancer therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Changes in environmental and engineered conditions alter the plasma membrane lipidome of fractured shale bacteria

ABSTRACT Microorganisms that persist in fractured shale reservoirs cause several problems including secreting foul gases and forming biofilms. Current biocontrol measures often fail due to limited knowledge of their in situ activities. The plasma membrane protects the cell, mediates many of its critical functions, and responds to intracellular cues and ecological perturbations through physicochemical modifications. As such, it provides valuable insight into the physiological adaptation of microorganisms in disturbed environmental systems. Here, we (i) demonstrate how changes in salinity and hydraulic retention time (HRT) influence the plasma membrane intact polar lipid (IPL) chemistry of model bacterium, Halanaerobium congolense WG10, and mixed microbial consortia enriched from shale-produced fluids and (ii) elucidate adjustments in membrane IPL chemistry during biofilm growth relative to planktonic cells. We incubated H. congolense WG10 in chemostats under three salinities (7%, 13%, and 20% NaCl), operated under three HRTs (19.2, 24, and 48 h), and in drip flow biofilm reactors under the same salinity gradients. Also, mixed microbial consortia in produced fluids were enriched in triplicate chemostat vessels under three HRTs (19.2, 24, and 72 h) and biofilm reactors. Lipids were analyzed by ultra high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Our results show that phosphatidylglycerols, cardiolipins, and phosphatidylethanolamines were predominantly enriched in planktonic H. congolense WG10 cells grown at hypersalinity (20%) compared to optimum (13%). In addition, several zwitterionic phosphatidylcholines and phosphatidylethanolamines were higher in abundance during biofilm growth. These observations suggest that microbial adaptation and biofilm formation in fractured shale are enabled by strategic plasma membrane IPL chemistry adjustments. IMPORTANCE Microorganisms inadvertently introduced into the shale reservoir during fracturing face multiple stressors including brine-level salinities and starvation. However, some anaerobic halotolerant bacteria adapt and persist for long periods of time. They produce hydrogen sulfide, which sours the reservoir and corrodes engineering infrastructure. In addition, they form biofilms on rock matrices, which decrease shale permeability and clog fracture networks. These reduce well productivity and increase extraction costs. Under stress, microbes remodel their plasma membrane to optimize its roles in protection and mediating cellular processes such as signaling, transport, and energy metabolism. Hence, by observing changes in the membrane lipidome of model shale bacteria, Halanaerobium congolense WG10, and mixed consortia enriched from produced fluids under varying subsurface conditions and growth modes, we provide insight that advances our knowledge of the fractured shale biosystem. We also offer data-driven recommendations for improving biocontrol efficacy and the efficiency of energy recovery from unconventional formations.

03 NATURAL GAS↗
DOE OSTI2020

Insights of Molecular Mechanism of Xylem Development in Five Black Poplar Cultivars

Black poplar (Populus deltoides, P. nigra, and their hybrids) is the main poplar cultivars in China. It offers interesting options of large-scale biomass production for bioenergy due to its rapid growth and high yield. Poplar wood properties were associated with chemical components and physical structures during wood formation. In this study, five poplar cultivars, P. euramericana ‘Zhonglin46’ (Pe1), P. euramericana ‘Guariento’ (Pe2), P. nigra ‘N179’ (Pn1), P. deltoides ‘Danhong’ (Pd1), and P. deltoides ‘Nanyang’ (Pd2), were used to explore the molecular mechanism of xylem development. We analyzed the structural differences of developing xylem in the five cultivars and profiled the transcriptome-wide gene expression patterns through RNA sequencing. The cross sections of the developing xylem showed that the cell wall thickness of developed fiber in Pd1 was thickest and the number of xylem vessels of Pn1 was the least. A total of 10,331 differentially expressed genes were identified among 10 pairwise comparisons of the five cultivars, most of them were related to programmed cell death and secondary cell wall thickening. K-means cluster analysis and Gene Ontology enrichment analysis showed that the genes highly expressed in Pd1 were related to nucleotide decomposition, metabolic process, transferase, and microtubule cytoskeleton; whereas the genes highly expressed in Pn1 were involved in cell wall macromolecule decomposition and polysaccharide binding processes. Based on a weighted gene co-expression network analysis, a large number of candidate regulators for xylem development were identified. And their potential regulatory roles to cell wall biosynthesis genes were validated by a transient overexpression system. This study provides a set of promising candidate regulators for genetic engineering to improve feedstock and enhance biofuel conversion in the bioenergy crop Populus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Gene regulatory networks controlling carbohydrate selective deconstruction pathways in fungi

The work performed at Clark University (PI, David Hibbett) was a subcomponent of the research lead by Jonathan Schilling at University of Minnesota (award number DE-SC0019427). The overall goal of this project was to address how fungi metabolize lignocellulose. Specifically, we targeted a carbohydrate-selective group of fungi known as 'brown rot' fungi that are well-aligned to be harness for bioconversion to biofuels and other products. These organisms orchestrate a two-step mechanism that initiates decomposition using oxidative radical-based chemistry and follows with enzymatic attack. We have helped characterize that this mechanism occurs in this sequence, but currently lack the fundamental regulatory information needed to harness these fungi for application. Thus, the major goal of this project was to use systems biology to create an integrated model of brown rot wood decay that couples fungal gene regulation with the metabolite feedbacks used to coordinate a two-step oxidative-hydrolytic mechanism. The research at Clark University focused on phylogenomic analyses of data produced by other project partners. Hence, the Clark component of the research was staged to initiate somewhat after that in other partner laboratories. The major Clark-based accomplishment was to advise on selection of fungal species for analyses of brown rot decay chemistry, and to interpret results in a phylogenetic context. The Clark University group also performed complementary analyses of gene families encoding plant cell wall-degrading enzymes in the the basidiomycete genus Lentinula, as well as analyses of substrate-specific gene expression and RNA editing in brown rot fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Motivation: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems such as protein complexes, metabolic reactions, and signal transduction pathways. Hypergraphs are generalizations of graphs that naturally model multi-way interactions in data, and we therefore seek to understand how they can more faithfully identify, and potentially predict, complex relationships in genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges are differentially expressed genes and vertices represent conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Our results demonstrate the utility of using hypergraphs to represent complex biological systems, and highlight potentially interesting biological results about host response to highly pathogenic viruses.

systems biology, hypergraph, viral infection, biol↗
DOE OSTI2021

Where Have All of the Electrons Gone? Understanding the Role of Alternative Electron Flow and O 2 Reduction in Balancing Cellular Redox (Final Technical Report)

An informed understanding of the fundamentals of light-driven electron transfer reactions in photoautotrophic organisms is necessary to enable improved photosynthetic efficiencies for the production of renewable fuels and novel biomaterials. To obtain high photosynthetic yields, light energy must be efficiently coupled to the fixation of CO 2 . Sub-optimal environmental conditions and metabolic routing (caused by blocks in biosynthetic routes) can severely impact the conversion of light energy to biomass and lead to reactive oxygen production, which in turn can cause cellular damage and productivity losses. Hence, plants, algae, and photosynthetic bacteria have evolved a network of alternative outlets to sustain the flow of photosynthetically derived-electrons. Our research was focused on the nature and integration of these outlets. The data obtained in this project will inform efforts to rationally engineer crop plants and algae to improve photosynthetic yields by enhancing electron transfer reactions to CO 2 reduction and targeted biomass accumulation. A major project research thrust was focused on identifying and quantifying the flow of photosynthetic reductant through electron transfer circuits that result in the light-dependent reduction of O 2 . New energy management strategies were identified that are used when normal carbon assimilation pathways are compromised due to nutrient deprivation, and/or by a reduction in starch synthesis/carbon storage, all conditions resulting in highly reduced intracellular redox pools. The green alga Chlamydomonas reinhardtii, and likely many other algae, have multiple O 2 -reducing pathways that play critical roles in maintaining cellular metabolic balance and scavenging electrons that could potentially cause cellular damage, which in some instances leads to reduced photosynthetic yields but increased fitness. We explored the activities of three essential outlets associated with Chlamydomonas reinhardtii photosynthetic electron transport: (1) reduction of O 2 to H 2 O through Flavodiiron proteins (FLVs) and (2) Plastid Terminal Oxidases (PTOX), and (3) the synthesis of starch. Real-time measurements of O 2 exchange demonstrated that FLVs immediately engage during dark to light transitions, allowing electron transport when the CBBC is not fully activated. Under these conditions, we quantified, for the first time, maximal FLV activity and its overall capacity to direct photosynthetic electrons towards O 2 reduction. However, when starch synthesis is compromised, a greater proportion of electrons is directed toward O 2 reduction through the FLVs, while PTOX, which is sensitive to the PQ pool redox state, is activated. This suggests, that starch synthesis has an important role in priming/regulating CBBC and electron transport. We also identified a biological ‘switch’ in the green alga Chlamydomonas reinhardtii that reversibly restricts photosynthetic electron transport (PET) at the cytochrome b 6 f complex when reductant and ATP generated by PET are in excess of the capacity of carbon metabolism to utilize these products; we specifically show a restriction at this switch when sta6 mutant cells, which cannot synthesize starch, are limited for nitrogen (growth inhibition) and subjected to a dark to light transition. This restriction causes diminished electron flow to PSI, which prevents PSI photodamage, and the plastid alternative oxidase (PTOX) becomes fully activated, serving as an electron valve that dissipates excitation energy absorbed by PSII, thereby lessening PSII photoinhibition. Furthermore, illumination of the cells following the dark acclimation gradually diminishes the restriction at the switch. Future engineering of these switches may allow more effective electron transfer to lipid (biofuel) pathways and diminish the number of electrons “wasted” in the reduction of O 2 to water. Lastly, we explored metabolic routing of electrons during algal fermentation and discovered multiple novel pathways that are activated when the preferred anoxic routes are blocked. These provide valuable products (e.g. lactate, glycerol) that can be used in broad portfolio of biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism

ABSTRACT Trichoderma species are known for their mycoparasitic activity against phytopathogenic fungi that cause significant economic losses in agriculture. During mycoparasitism, Trichoderma spp. recognize molecules produced by the host fungus and release secondary metabolites and hydrolytic enzymes to kill and degrade the host’s cell wall. Here, we explored the participation of the Trichoderma atroviride RNAi machinery in the interaction with six phytopathogenic fungi of economic importance. We determined that both Argonaute-3 and Dicer-2 play an essential role during mycoparasitism. Using an RNA-Seq approach, we identified that perception, detox, and cell wall degradation depend on the T. atroviride -RNAi when interacting with Alternaria alternata, Rhizoctonia solani AG2 , and R. solani AG5. Furthermore, we constructed a gene co-expression network that provides evidence of two gene modules regulated by RNAi, which play crucial roles in essential processes during mycoparasitism. In addition, based on small RNA-seq, we conclude that siRNAs regulate amino acid and carbon metabolism and communication during the Trichoderma -host interaction. Interestingly, our data suggest that siRNAs might regulate allorecognition ( het ) and transport genes in a cross-species manner. Thus, these results reveal a fine-tuned regulation in T. atroviride dependent on siRNAs that is essential during the biocontrol of phytopathogenic fungi, showing a greater complexity of this process than previously established. IMPORTANCE There is an increasing need for plant disease control without chemical pesticides to avoid environmental pollution and resistance, and the health risks associated with the application of pesticides are increasing. Employing Trichoderma species in agriculture to control fungal diseases is an alternative plant protection strategy that overcomes these issues without utilizing chemical fungicides. Therefore, understanding the biocontrol mechanisms used by Trichoderma species to antagonize other fungi is critical. Although there has been extensive research about the mechanisms involved in the mycoparasitic capability of Trichoderma species, there are still unsolved questions related to how Trichoderma regulates recognition, attack, and defense mechanisms during interaction with a fungal host. In this work, we report that the Argonaute and Dicer components of the RNAi machinery and the small RNAs they process are essential for gene regulation during mycoparasitism by Trichoderma atroviride .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Physical, resource supply, and biological controls on nutrient processing along the river continuum

Nutrient impairment has led to damages to US surface and groundwater systems in excess of 100 billion dollars per year. Therefore, there is a strong need to develop methods to predict the transport, uptake, and export of nutrients along fluvial networks. We present results that are based on a data-driven mechanistic understanding of three factors that largely control nutrient uptake and export: 1) interactions between transport-related processes (mass transfer to metabolically active zones), 2) resource supply dynamics (nutrient concentration, stoichiometric constraints, etc.), and 3) biological controls (microbial community structure and function). Our results were generated from column experiments conducted along the Jemez River-Rio Grande continuum, which spans four orders of magnitude in mean annual discharge, more than 2000 m in altitude, and more than 500 km of stream longitude. Two resource supply injections were performed on each of the columns, i.e., a nitrate only addition, followed by a stoichiometrically ‘balanced’ 106Carbon:16Nitrogen:1Phosphorus addition. We quantified NO3-N uptake kinetics while constraining three variables: stream order, sediment type and type of injection (N vs stoichiometrically ‘balanced’ C:N:P). Following the laboratory nutrient uptake experiments, the columns were destructively sampled and the contents were homogenized to collect subsamples for DNA sequencing. Amplicon analysis was carried out as described by the Earth Microbiome Protocol for 16s and ITS sequencing.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

BETO 2021 Peer Review: Algae Biotechnology Partnership - Technology Area Session: Advanced Algae Systems

Development of advanced genetic and genomic tools for targeted algal metabolic engineering pursuits will be integral to achieving target biomass productivity and, ultimately, the BETO goal of cost-competitive biofuels derived from algal biomass by 2022. However, at present, broad-host-range tool development is currently hindered by strain-specific negative regulatory mechanisms. Indeed, the biological processes controlling algal transcription and translation are subject to complex host regulation, which often presents hurdles for targeted genetic engineering strategies. Advanced genetic approaches offer a means to rewire these regulatory systems and/or introduce novel functionality into algal biocatalysts. Synthetic systems biology approaches also present a means to construct novel genetic regulatory networks and rewire natural biological systems to establish an “orthogonal central dogma,” wherein non-native control elements are introduced into or evolved in host microbes for bypass of host control. To this end, the Algae Biotechnology Partnership aims to develop advanced genetic editing tools and synthetic and orthogonal genetic regulatory systems to enable universal metabolic engineering strategies in top-candidate deployment algal strains. Successful development will ultimately open the door for targeted strain-engineering strategies, aimed at maximizing algal outdoor biomass production, composition, and strain robustness.

biocatalysis↗
DOE OSTI2025

Challenges in integrating dissolved organic matter chemodiversity into kinetic models of soil respiration

The chemodiversity of dissolved organic matter (DOM) in soil has been proposed to influence the microbial metabolism and fate of belowground organic carbon (C). However, integrating DOM chemistry into soil C cycle models to improve predictions of C stocks and fluxes—beyond simply considering DOM pool size—remains a challenge. While recent research suggests that incorporating DOM chemodiversity into models can improve predictions of microbial respiration, there is still a lack of mechanistic understanding describing how DOM chemodiversity affects microbial metabolism and soil respiration. Here, we evaluated whether DOM chemodiversity was a determinant of soil respiration using paired measurements of high-resolution DOM chemistry, obtained from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), and potential soil respiration rates from across the United States (U.S.), all data provided by the Molecular Observation Network. Our objectives were to (1) assess statistical relationships between DOM chemodiversity and microbial respiration, and (2) evaluate the ability of kinetic models to leverage DOM chemistry to explain empirical relationships found in statistical models. Statistical regressions revealed that DOM chemodiversity (alpha diversity) was nonlinearly related to potential soil respiration rates, both independently and through its interactions with DOM and total C concentrations. In soils with relatively high DOM but low total C concentrations, potential soil respiration rates were negatively correlated with DOM alpha diversity, whereas in soils with relatively low DOM and high total C concentrations showed the opposite trend. However, when metabolic transition theory kinetic models were modified to include chemodiversity, their performance was comparable to traditional Monod kinetics approaches, which simulate respiration rates as a function of DOM concentration. The inability to account for nonlinearities in DOM chemodiversity–respiration relationships highlight an opportunity to advance substrate uptake kinetics by establishing causal links between DOM chemodiversity, microbial metabolism trade-offs, and potential interactions under varied environmental conditions.

Bioenergetic model↗
NASA NTRS2019

Estuarine Dissolved Organic Carbon Flux From Space: With Application to Chesapeake and Delaware Bays

This study uses a neural network model trained with in situ data, combined with satellite data and hydrodynamic model products, to compute the daily estuarine export of dissolved organic carbon (DOC) at the mouths of Chesapeake Bay (CB) and Delaware Bay (DB) from 2007 to 2011. Both bays show large flux variability with highest fluxes in spring and lowest in fall as well as interannual flux variability (0.18 and 0.27 Tg C/year in 2008 and 2010 for CB; 0.04 and 0.09 Tg C/year in 2008 and 2011 for DB). Based on previous estimates of total organic carbon (TOCexp) exported by all Mid-Atlantic Bight estuaries (1.2 Tg C/year), the DOC export (CB + DB) of 0.3 Tg C/year estimated here corresponds to 25% of the TOCexp. Spatial and temporal covariations of velocity and DOC concentration provide contributions to the flux, with larger spatial influence. Differences in the discharge of fresh water into the bays (74 billion cu. m/year for CB and 21 billion cu. m/year for DB) and their geomorphologies are major drivers of the differences in DOC fluxes for these two systems. Terrestrial DOC inputs are similar to the export of DOC at the bay mouths at annual and longer time scales but diverge significantly at shorter time scales (days to months). Future efforts will expand to the Mid-Atlantic Bight and Gulf of Maine, and its major rivers and estuaries, in combination with coupled terrestrial-estuarine-ocean biogeochemical models that include effects of climate change, such as warming and CO2 increase.

Estuarine DOC export↗
DOE OSTI2022

Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes

Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Tensegrity II. How structural networks influence cellular information processing networks

The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

Review↗
DOE OSTI2023

Metabolic and transcriptomic study of pennycress natural variation identifies targets for oil improvement

Pennycress (Thlaspi arvense L.), a member of the Brassicaceae family, produces seed oil high in erucic acid, suitable for biodiesel and aviation fuel. Although pennycress, a winter annual, could be grown as a dedicated bioenergy crop, an increase in its seed oil content is required to improve its economic competitiveness. The success of crop improvement relies upon finding the right combination of biomarkers and targets, and the best genetic engineering and/or breeding strategies. In this work, we combined biomass composition with metabolomic and transcriptomic studies of developing embryos from 22 pennycress natural variants to identify targets for oil improvement. The selected accession collection presented diverse levels of fatty acids at maturity ranging from 29% to 41%. Pearson correlation analyses, weighted gene co‐expression network analysis and biomarker identifications were used as complementary approaches to detect associations between metabolite level or gene expression and oil content at maturity. The results indicated that improving seed oil content can lead to a concomitant increase in the proportion of erucic acid without affecting the weight of embryos. Processes, such as carbon partitioning towards the chloroplast, lipid metabolism, photosynthesis, and a tight control of nitrogen availability, were found to be key for oil improvement in pennycress. Besides identifying specific targets, our results also provide guidance regarding the best timing for their modification, early or middle maturation. Thus, this work lays out promising strategies, specific for pennycress, to accelerate the successful development of lines with increased seed oil content for biofuel applications.

59 BASIC BIOLOGICAL SCIENCES↗