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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Wetlands harbor lactic acid-driven chain elongators

Wetlands are globally significant carbon storage hotspots. Recent research has suggested that microbially derived metabolites may contribute to soil organic matter formation. Identifying pathways driving the formation of such metabolites is critical to understand the global impact of wetland carbon cycling. Here, we evaluate the presence of chain-elongating organisms converting two to three carbon compounds (i.e., lactic and acetic acid) to medium-chain carboxylic acids (MCCA; i.e., six-carbon caproic acid) in wetland soils. We demonstrate the enrichment of a lactic acid-driven chain-elongating community from wetland soils producing a mixture of butyric and caproic acid. The enriched community was dominated by Clostridiaceae, Ruminococcaceae, and Lachnospiraceae, three families with known chain elongators. Amplicon sequencing identified three Ruminococcaceae and one Clostridiaceae zero-radius OTU (zOTU) that were (i) present in the soil, (ii) enriched over 1% relative abundance in the bioreactor, and (iii) were closely related to known chain elongators. Moreover, close relatives of the three Ruminococcaceae zOTU were also observed in several other wetland microbiomes. From this observation, we conclude that close relatives of known chain elongators, potentially capable of lactic acid-driven MCCA production themselves, are present in wetland soils. This observation may have implications for our understanding of carbon cycling and storage in wetland ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Biochemical Characterization of Rice Xylan Biosynthetic Enzymes in Determining Xylan Chain Elongation and Substitutions

Abstract Grass xylan consists of a linear chain of β-1,4-linked xylosyl residues that often form domains substituted only with either arabinofuranose (Araf) or glucuronic acid (GlcA)/methylglucuronic acid (MeGlcA) residues, and it lacks the unique reducing end tetrasaccharide sequence found in dicot xylan. The mechanism of how grass xylan backbone elongation is initiated and how its distinctive substitution pattern is determined remains elusive. Here, we performed biochemical characterization of rice xylan biosynthetic enzymes, including xylan synthases, glucuronyltransferases and methyltransferases. Activity assays of rice xylan synthases demonstrated that they required short xylooligomers as acceptors for their activities. While rice xylan glucuronyltransferases effectively glucuronidated unsubstituted xylohexaose acceptors, they transferred little GlcA residues onto (Araf)-substituted xylohexaoses and rice xylan 3-O-arabinosyltransferase could not arabinosylate GlcA-substituted xylohexaoses, indicating that their intrinsic biochemical properties may contribute to the distinctive substitution patterns of rice xylan. In addition, we found that rice xylan methyltransferase exhibited a low substrate binding affinity, which may explain the partial GlcA methylation in rice xylan. Furthermore, immunolocalization of xylan in xylem cells of both rice and Arabidopsis showed that it was deposited together with cellulose in secondary walls without forming xylan-rich nanodomains. Together, our findings provide new insights into the biochemical mechanisms underlying xylan backbone elongation and substitutions in grass species.

Cell Biology↗
DOE OSTI2025

Development of emerging model microorganisms: Megasphaera elsdenii for biomass and organic acid upgrading to fuels and chemicals

The metabolic diversity of microorganisms in nature represents a largely untapped source of valuable compounds that are difficult or impossible to produce in the limited number of available model systems. Efforts to produce longer-chain alcohols, such as hexanol, in organisms like Escherichia coli have met with limited success; production of C6 and larger products remains low, highlighting the challenges of extending chain elongation pathways beyond a single cycle. Megasphaera elsdenii naturally condenses acetyl-CoA to efficiently generate C4–C8 organic acids, making it a promising candidate for producing fuels and chemicals from lactate and plant-derived carbohydrates. This high native flux through the chain elongation pathway offers the potential for higher yields and titers of medium-chain products, such as hexanol, compared to conventional hosts. Recent advances—most notably the development of a transformation method for M. elsdenii—have further opened the organism to detailed physiological studies and bioengineering. While full development of M. elsdenii as a hexanol-producing platform was not achieved, significant progress was made in understanding its metabolism and building foundational genetic tools for future engineering.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Higher-order interaction effects among operating conditions and feedstocks shape reactor microbiomes and fatty acid production profiles

Arrested anaerobic digestion (AAD) offers a promising route for producing fatty acids (FAs) from organic residues, yet optimal conditions for selectively generating medium-chain fatty acids (MCFAs) remain poorly defined. Here, we systematically evaluated the main and interaction effects of pH (5, 7, 9), feedstock (food waste, manure), temperature (35 and 45 °C), and inoculum source on microbiome composition and FA production. Anaerobic digester sludge and a novel bison rumen inoculum were compared. Significant higher-order interactions among operating parameters governed FA profiles and microbiome structure. Butyric acid production was driven by a three-way interaction among pH, feedstock, and temperature (p < 0.001), with maximum concentrations achieved in food waste reactors at pH 5.0 and 35 °C (1.2 ± 0.1 g L −1 with sludge and 1.1 ± 0.3 g L −1 with rumen). MCFA production exhibited significant four-way interactions (p < 0.1 to p < 0.001). At 45 °C and pH 5.0, inoculum source tuned MCFA selectivity: sludge favored pentanoic acid (0.4 ± 0.1 g L −1 ), whereas rumen favored hexanoic and heptanoic acids (up to 0.4 ± 0.2 g L −1 ). Manure reactors produced < 0.2 g L −1 MCFAs under all conditions. Genera, including Megasphaera, Prevotella, and Lactobacillus, were associated with production of specific MCFAs. PICRUSt2-based pathway predictions were consistent with MCFA production patterns and suggested a potential role for lactic acid–driven chain elongation pathways. This study provides insights into how interacting operating conditions shape AAD microbiomes, their FA profiles, and advances the trajectory of research aimed at engineering robust and controllable microbiomes for waste valorization.

09 BIOMASS FUELS↗
DOE OSTI2026

Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and Conversion

Lignocellulosic plant biomass is a widely-abundant renewable resource that can be harnessed for value-added production of fuels & chemicals. While microbes have been engineered to breakdown lignocellulose and turn released sugars into products, this remains an energy-intensive process that requires expensive pre-treatment and separation steps. Furthermore, it is difficult to engineer all desirable traits for breakdown and conversion into one organism. This project developed a new strategy that relies on microbial partnerships formed in the herbivore rumen to liberate sugars from crude plant biomass and convert that sugar to value-added chemicals. Microbial consortia consisting of fungi, bacteria, and archaea form tight associations in the herbivore rumen, which divide-and-conquer the difficult tasks of biomass breakdown. This project leveraged a “synthetic rumen” consortium composed of anaerobic fungi and chain-elongating bacteria to study which metabolites are shared and exchanged between microbes and identify strategies to bolster lignocellulose conversion to value-added products. Our approach developed high-throughput systems and synthetic biology approaches to realize stable synthetic consortia that route lignocellulosic carbon into short and medium chain fatty acids (SCFAs/MCFAs) rather than methane. Key research objectives were to (1) design and predict anaerobic fungal and bacterial consortia that efficiently convert lignocellulosic biomass into medium-chain fatty acids (MCFAs), (2) understand how fermentation parameters and microbe-microbe interactions regulate and drive microbiome metabolic fluxes, and (3) use genomic editing to alter the fermentation byproducts of anaerobic fungi and bolster MCFA titers and yields.

09 BIOMASS FUELS↗
NASA NTRS1998

Polymerization on the rocks: theoretical introduction

It is difficult if not impossible to synthesize long polymers of amino acids, nucleotides, etc., in homogeneous aqueous solution. We suggest that long polymers were synthesized on the surface of minerals in a prebiotic process analogous to solid-phase synthesis. Provided that the affinity of a mineral for an oligomer increases with the length of the oligomer, adsorption must become essentially irreversible for sufficiently long oligomers. Irreversibly adsorbed oligomers may be elongated indefinitely by repeated cycles in which the mineral with its adsorbed oligomers is first incubated with activated monomers and then washed free of deactivated monomer and side-products. We discuss in some detail the formation of oligomers of negatively-charged amino acids such as glutamic acid on anion-exchange minerals such as hydroxylapatite or illite. We show that the average length of adsorbed oligomers at steady state, n, depends on the balance between the rate of chain elongation and the rate of hydrolysis, and we derive a very approximate formula for n.

NASA Discipline Exobiology↗
DOE OSTI2024

Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture

Organic-rich industrial residues can serve as renewable feedstocks for the generation of useful products by microbial fermentation. We investigated fermenting communities enriched in a mixture of ultra-filtered milk permeate (UFMP) and acid whey from cottage cheese (CAW), two dairy coproducts rich in lactose. To evaluate how operational pH and temperature affect microbial communities and fermentation products, we operated 12 bioreactors for 140 days, each fed a 1:1 mixture of UFMP and CAW at either 35 °C or 50 °C and at either a pH of 4.8 or 5.5. The bioreactors operated at a pH of 4.8 resulted in the incomplete conversion of lactose, while those operated at a pH of 5.5 consistently fermented lactose, primarily into lactic, acetic, and hexanoic acids. The metagenomic analyses revealed that microbial communities obtained at a pH of 5.5 were dominated by lactic acid-producing organisms. Additionally, an inverse relationship was found between the abundance of chain elongating organisms and lactic acid accumulation, with 50 °C reducing the abundance of these organisms and enhancing lactic acid yields. We conclude that the pH and temperature are important determinants of the fermentation of dairy coproducts with a pH of 5.5 and 50 °C yielding the most promising results for lactic acid production. Additional research is required to better understand the factors affecting functional consistency of the process.

Biotechnology & Applied Microbiology↗
NASA NTRS1980

Three-dimensional structure of Escherichia coli initiator tRNA/f//Met/

The crystal structure of Escherichia coli tRNA(f)(Met), an initiator transfer RNA, has been determined. While grossly similar to that of the chain-elongating yeast tRNA(Phe), there are three major differences. One involves the folding of the anticodon loop; in particular, the position of the constant uridine, U33. This difference was unexpected and may be of functional significance.

Woo, N. H.↗
NASA NTRS1993

Is ligation the only solution to the pyrophosphate problem?

Pyrophosphate linkages are easily formed during the nonenzymatic oligomerization of activated nucleotides. They often form `caps' which terminate an oligonucleotide with a 5'-5' pyrophosphate. Owing to their structural resemblance to the intermediates in enzymatic ligation reactions, it has been suggested that pyrophosphate caps might have been capable of acting as activating groups in chain elongation processes. We argue that an alternative possibility would have been the specific hydrolysis of pyrophosphates.

Visscher, J.↗
NASA NTRS1998

Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families

As the amount of available sequence data increases, it becomes apparent that our understanding of translation initiation is far from comprehensive and that prior conclusions concerning the origin of the process are wrong. Contrary to earlier conclusions, key elements of translation initiation originated at the Universal Ancestor stage, for homologous counterparts exist in all three primary taxa. Herein, we explore the evolutionary relationships among the components of bacterial initiation factor 2 (IF-2) and eukaryotic IF-2 (eIF-2)/eIF-2B, i.e., the initiation factors involved in introducing the initiator tRNA into the translation mechanism and performing the first step in the peptide chain elongation cycle. All Archaea appear to posses a fully functional eIF-2 molecule, but they lack the associated GTP recycling function, eIF-2B (a five-subunit molecule). Yet, the Archaea do posses members of the gene family defined by the (related) eIF-2B subunits alpha, beta, and delta, although these are not specifically related to any of the three eukaryotic subunits. Additional members of this family also occur in some (but by no means all) Bacteria and even in some eukaryotes. The functional significance of the other members of this family is unclear and requires experimental resolution. Similarly, the occurrence of bacterial IF-2-like molecules in all Archaea and in some eukaryotes further complicates the picture of translation initiation. Overall, these data lend further support to the suggestion that the rudiments of translation initiation were present at the Universal Ancestor stage.

NASA Discipline Exobiology↗
NASA NTRS2014

Assessing the Origins of Aliphatic Amines in the Murchison Meteorite from their Compound-Specific Carbon Isotopic Ratios and Enantiomeric Composition

The study of meteoritic organic compounds provides a unique window into the chemical inventory of the early Solar System and prebiotic chemistry that may have been important for the origin of life on Earth. Multiple families of organic compounds have been extracted from the Murchison meteorite, which is one of the most thoroughly studied carbonaceous chondrites. The amino acids extracted from Murchison have been extensively analyzed, including measurements of non-terrestrial stable isotopic ratios and discoveries of L-enantiomeric excesses for alpha-dialkyl amino acids, notably isovaline. However, although the isotopic signatures of bulk amine-containing fractions have been measured, the isotopic ratios and enantiomeric composition of individual aliphatic amines, compounds that are chemically related to amino acids, remain unknown. Here, we report a novel method for the extraction, separation, identification and quantitation of aliphatic monoamines extracted from the Murchison meteorite. Our results show a complete suite of structural isomers, with a larger concentration of methylamine and ethylamine and decreasing amine concentrations with increasing carbon number. The carbon isotopic compositions of fourteen meteoritic aliphatic monoamines were measured, with delta C-13 values ranging from +21% to +129%, showing a decrease in C-13 with increasing carbon number, a relationship that may be consistent with the chain elongation mechanism under kinetic control previously proposed for meteoritic amino acids. We also found the enantiomeric composition of sec-butylamine, a structural analog to isovaline, was racemic within error, while the isovaline extracted from the same Murchison piece showed an L-enantiomeric excess of 9.7; this result suggested that processes leading to enantiomeric excess in the amino acid did not affect the amine. We used these collective data to assess the primordial synthetic origins of these meteoritic aliphatic amines and their potential linkage to meteoritic amino acids.

prebiotic chemistry↗
DOE OSTI2025

Feedstock Variability: Differences Among Biomass Anatomical Fractions and Tissues

Corn stover is a versatile feedstock for producing biofuels and other sustainable products. However, its diverse chemical and physical attributes can hinder the processes that convert it into these compounds. The composition of corn stover varies according to factors including corn plant variety, cultivation conditions and maturity at harvest. In essence, corn stover consists of the polymers cellulose, hemicellulose and lignin. The structural core of plant cell walls consists of elongated chains of glucose molecules arranged in bundles of cellulose. Additionally, lower concentrations of hemicellulose, a complex carbohydrate composed of various sugars, form part of the matrix surrounding cellulose bundles. Lignin is a complex aromatic polymer that reinforces plant cell walls. Corn stover generally comprises 40%-50% cellulose, 20%-30% hemicellulose, and 20%-30% lignin. The ratios of these components vary based on the specific type of corn plant and the growth conditions. For example, corn plants cultivated in drought conditions exhibit higher lignin levels than those grown under optimal conditions. The compositional diversity resulting from growth conditions is most pronounced among the different anatomical fractions of the corn plant. Understanding and accommodating the variation among the anatomical fractions of corn stover can enhance the effective utilization of this resource.

09 BIOMASS FUELS↗
NASA NTRS1999

Oligomerization of L-gamma-carboxyglutamic acid

Unlike glutamic acid, L-gamma-carboxyglutamic acid does not oligomerize efficiently when treated with carbonyldiimidazole in aqueous solution. However, divalent ions such as Mg2+ catalyze the reaction, and lead to the formation of oligomers in good yield. In the presence of hydroxylapatite, L-gamma-carboxyglutamic acid oligomerizes efficiently in a reaction that proceeds in the absence of divalent ions but is further catalyzed when they are present. After 'feeding' 50 times with activated amino acid in the presence of the Mg2+ ion, oligomers longer than the 20-mer could be detected. The effect of hydroxylapatite on peptide elongation is very sensitive to the nature of the activated amino acid and the acceptor peptide. Glutamic acid oligomerizes more efficiently than L-gamma-carboxyglutamic acid on hydroxylapatite and adds more efficiently to decaglutamic acid in solution. One might, therefore, expect that glutamic acid would add more efficiently than L-gamma-carboxyglutamic acid to decaglutamic acid on hydroxylapatite. The contrary is true--the addition of L-gamma-carboxyglutamic acid is substantially more efficient. This suggests that oligomerization on the surface of hydroxylapatite depends on the detailed match between the structure of the surface of the mineral and the structure of the oligomer.

Non-NASA Center↗
NASA NTRS1971

Lava tubes and channels in the Lunar Marius Hills.

The Marius Hills region, a volcanic plateau in Oceanus Procellarum, contains numerous rilles, rille-like structures, and chains of elongate craters. Most of these structures characteristically: (1) originate on or near irregular shaped craters associated with features previously interpreted as volcanic domes, (2) trend downslope onto Plateau Plains, (3) generally taper in width and become shallower, (4) are often discontinuous, (5) occupy the center, or apparent crest of a broad ridge, (6) may contain cut-off branches and distributary structures, and (7) may have local reversals in longitudinal slope. Structures having these characteristics are interpreted to be lava channels or partly collapsed lava tubes. Terrestrial lava tubes form exclusively, and commonly, in fluid basalt flows. Recent evidence indicates that viscosities of lunar mare 'basalt' lava flows were conducive for lava tube formation. Terrestrial analogs are offered for structures described in the Marius Hills.

Greeley, R.↗
NASA NTRS2020

Shape Estimation for Elongated Deformable Object using B-spline Chained Multiple Random Matrices Model

In this paper, a B-spline chained multiple random matrix models (RMMs) representation is proposed to model geometric characteristics of an elongated deformable object. The hyper degrees of freedom structure of the elongated deformable object make its shape estimation challenging. Based on the likelihood function of the proposed B-spline chained multiple RMMs, an expectation-maximization (EM) method is derived to estimate the shape of the elongated deformable object. A split and merge method based on the Euclidean minimum spanning tree (EMST) is proposed to provide initialization for the EM algorithm. The proposed algorithm is evaluated for the shape estimation of the elongated deformable objects in scenarios, such as the static rope with various configurations (including configurations with intersection), the continuous manipulation of a rope and a plastic tube, and the assembly of two plastic tubes. The execution time is computed and the accuracy of the shape estimation results is evaluated based on the comparisons between the estimated width values and its ground-truth, and the intersection over union (IoU) metric.

Gang Yao↗
DOE OSTI2025

Fluorinated polythiophenes with ester side chains for boosting the V OC and efficiency in non-fullerene polymer solar cells

As the power conversion efficiency (PCE) of organic photovoltaics (OPVs) approximates the 19 % threshold, wide bandgap (WBG) polythiophenes (PTs) have gained increasing attention due to their simple chemical structures and ease of synthesis, making them promising candidates for large-scale production. However, the benchmark polymer poly(3-hexylthiophene) (P3HT) is limited by its high-lying HOMO energy level, which restricts the open-circuit voltage (V OC ) in solar cells. Here, in this study, we introduce a novel series of PT derivatives (PDC8-T, PDC8-3T, PDC16-3T, and PDC16-3T-2F) featuring ester side chains designed to fine-tune electronic properties through a streamlined three-step synthesis. Additionally, we incorporated a π-spacer to reduce steric hindrance and elongated alkyl side chains to improve solubility and processability. Compared to P3HT, these PT derivatives demonstrate a significant reduction in HOMO energy levels, lowering by approximately 0.3–0.4 eV. Among them, PDC16-3T-2F—with fluorine atom substitution—achieves the lowest HOMO energy level, induces a coplanar molecular conformation, and enhances polymer aggregation behavior. We evaluated these PT derivatives in inverted non-fullerene bulk-heterojunction (NFA BHJ) OPVs. The PDC8-3T device showed a relatively low PCE of 0.69 %, with a V OC of 0.76 V, a short-circuit current density (J SC ) of 3.32 mA/cm 2 , and a fill factor (FF) of 27.3 %. In contrast, the PDC16-3T-2F device achieved an impressive PCE of 7.21 %, with a V OC of 0.85 V, a J SC of 14.60 mA/cm 2 , and an FF of 58.4 %. This remarkable improvement is attributed to the fluorine substitution, which not only enhances molecular orientation but also downshifts the HOMO energy level and further boosts the V OC . Hence, these molecular design strategies have led to a fibrillar bicontinuous interpenetrating network with optimal nanoscale phase separation within the active layer.

14 SOLAR ENERGY↗
NASA NTRS1977

Viking Observations of Phobos and Deimos: Preliminary Results

The improved resolution of the Viking images has led to the discovery of a number of unusual surface features on Phobos. The features include elongated rill-like depressions associated with the crater Stickney, chains and clusters of irregular elongated craters, and linear striations or grooves. Crater counts are also considered. A total of 27 craters ranging in size from 0.3 to 1.4 km are visible on the best Deimos frame available. Craters ranging from 50 m to 4.9 km in diameter can be observed on the best of the Phobos images.

Veverka, J.↗