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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Optimisation of root traits to provide enhanced ecosystem services in agricultural systems: A focus on cover crops

Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical and biotic properties of soil. However, cover crops, a group of plants that provide ecosystem services, can be utilised during fallow periods or used as an intercrop to restore soil health. The effectiveness of ecosystem services provided by cover crops varies widely as very little breeding has occurred in these species. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. In this study, we provide an overview of the range of belowground ecosystem services provided by cover crop roots: (1) soil structural remediation, (2) capture of soil resources and (3) maintenance of the rhizosphere and building of organic matter content. Based on the ecosystem services described, we outline current and promising phenotyping technologies and breeding strategies in cover crops that can enhance agricultural sustainability through improvement of root traits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A rhamnose-rich O-antigen of Paraburkholderia phymatum MP20 is required for symbiosis with Mimosa pudica

Paraburkholderia phymatum, a β-proteobacterium, forms a nitrogen-fixing symbiosis with many species of the large legume genus Mimosa as well as with common bean (Phaseolus vulgaris L.). Paraburkholderia are considered to have evolved nodulation independently from the well-studied α-proteobacteria symbionts of legumes. However, the detailed mechanisms important for β-rhizobia-legume symbiosis have not yet been determined. In this manuscript, we have sequenced the genome of P. phymatum MP20, a strain isolated from Mimosa pudica nodules, and utilized transposon mutagenesis to identify a mutant that showed delayed and ineffective nodulation of M. pudica. Further analysis revealed that the mutant strain produced an altered lipopolysaccharide lacking rhamnose containing O-antigen. Complementation with the wild-type gene restored the symbiosis. Microscopic analysis of the ineffective nodules showed that the mutant strain did not infect the cortical cells but was restricted to the endodermis. The results suggest that the O-antigen of P. phymatum is important for the bacterial infection of cortical cells and for nodule maturation. Further research will unveil the specific involvement of the glycosyltransferase gene in LPS biosynthesis and its impact on successful nodule formation by P. phymatum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia

The photosynthetic and diazotrophic cyanobacterium Trichodesmium is a key contributor to marine biogeochemical cycles in the subtropical-oligotrophic oceans. Trichodesmium form colonies that harbor a distinct microbial community in comparison to the surrounding seawater. The presence of their associated bacteria can expand Trichodesmium’s functional potential and is predicted to influence the cycling of carbon, nitrogen, phosphorus, and iron (C, N, P, and Fe). To link the bacteria associated with Trichodesmium to key functional traits and elucidate how community structure can influence nutrient cycling, we characterized Red Sea Trichodesmium colonies using metagenomics and metaproteomics. Colonies harbored bacteria that typically associate with algae and particles, such as the ubiquitous Alteromonas macleodii, but also lineages specific to Trichodesmium, such as members from the order Balneolales. The majority of associated bacteria were auxotrophic for different vitamins, indicating their dependency on vitamin production by Trichodesmium. The associated bacteria carry functional traits including siderophore biosynthesis, reduced phosphorus metabolism, and denitrification pathways. The analysis supports Trichodesmium as an active hotspot for C, N, P, Fe, and vitamin exchange. In turn, Trichodesmium may rely on associated bacteria to meet its high Fe demand as several lineages synthesize photolabile siderophores (e.g., vibrioferrin, rhizoferrin, petrobactin) which can enhance the bioavailability of particulate Fe to the entire consortium. Collectively, the results indicate that Trichodesmium colonies provide a structure where these interactions can take place. While further studies are required to clarify the exact nature of these interactions, Trichodesmium’s reliance on particle and algae-associated bacteria and the observed redundancy of key functional traits likely underpins the resilience of Trichodesmium within an ever-changing global environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Genetic Study of Nif -Associated Genes in a Hyperthermophilic Methanogen

Methanocaldococcus has been considered a model genus, but genetic tools have not been forthcoming until recently. Here, we develop and illustrate the utility of positive selection with either of two selective agents (simvastatin and neomycin), negative selection, generation of markerless in-frame deletion mutations, and genetic complementation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

Symbiotic associations between bacteria and leguminous plants lead to the formation of root nodules that fix nitrogen needed for sustainable agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet an integrated understanding of the extent of chromatin changes and transcriptional networks that functionally regulate gene expression associated with symbiosis remains poorly understood. In particular, analyses of early temporal events driving this symbiosis have only captured correlative relationships between regulators and targets at mRNA level. Here, we characterize changes in transcriptome and chromatin accessibility in the model legume Medicago truncatula, in response to rhizobial signals that trigger the formation of root nodules. We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with bacterial small molecules called lipo-chitooligosaccharides that trigger host symbiotic pathways of nodule development. Using a novel approach, dynamic regulatory module networks, we integrated ATAC-seq and RNA-seq time courses to predict cis-regulatory elements and transcription factors that most significantly contribute to transcriptomic changes associated with symbiosis. Regulators involved in auxin (IAA4-5, SHY2), ethylene (EIN3, ERF1), and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia. Our transcriptomic and chromatin accessibility datasets provide a valuable resource to understand the gene regulatory programs controlling the early stages of the dynamic process of symbiosis. The regulators identified provide potential targets for future experimental validation, and the engineering of nodulation in species is unable to establish that symbiosis naturally.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Plant Growth Promotion Diversity in Switchgrass-Colonizing, Diazotrophic Endophytes

Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass ( Panicum virgatum ), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1984

Tropospheric sources of NOx: lightning and biology

Laboratory experiments to quantify the global production of NOx (NO + NO2) in the troposphere due to atmospheric lightning and biogenic activity in soil are presented. These laboratory experiments, as well as other studies, suggest that the global production of NOx by lightning probably ranges between 2 and 20 MT(N)y-1 of NO and is strongly dependent on the total energy deposited by lightning, a quantity not well-known. In our laboratory experiments, nitrifying micro-organisms is soil were found to be a significant source of both NO and nitrous oxide (N2O). The measured production ratio of NO to N2O averaged 2-3 for oxygen partial pressures of 0.5-10%. Extrapolating these laboratory measurements to the global scale, which is somewhat risky, suggests that nitrifying micro-organisms in soil may account for as much as 10 MT(N) y-1 of NO. Additional experiments with denitrifying micro-organisms gave an NO to N2O production ratio ranging from 2 to 4 for an oxygen partial pressure of 0.5% and a ratio of less than unity for oxygen partial pressures ranging from 1 to 20%. The production of NO and N2O, normalized with respect to micro-organism number indicates that the production of both NO and N2O by denitrifying micro-organisms is at least an order of magnitude less than production by nitrifying micro-organisms for the micro-organisms studied.

Atmosphere/chemistry↗
NASA NTRS1994

Metabolic activity of microorganisms in evaporites

Crystalline salt is generally considered so hostile to most forms of life that it has been used for centuries as a preservative. Here, we present evidence that prokaryotes inhabiting a natural evaporite crust of halite and gypsum are metabolically active while inside the evaporite for at least 10 months. In situ measurements demonstrated that some of these "endoevaporitic" microorganisms (probably the cyanobacterium Synechococcus Nageli) fixed carbon and nitrogen. Denitrification was not observed. Our results quantified the slow microbial activity that can occur in salt crystals. Implications of this study include the possibility that microorganisms found in ancient evaporite deposits may have been part of an evaporite community.

NASA Discipline Exobiology↗
NASA NTRS1995

Mesoproterozoic Archaeoellipsoides: akinetes of heterocystous cyanobacteria

The genus Archaeoellipsoides Horodyski & Donaldson comprises large (up to 135 micrometers long) ellipsoidal and rod-shaped microfossils commonly found in silicified peritidal carbonates of Mesoproterozoic age. Based on morphometric and sedimentary comparisons with the akinetes of modern bloom-forming Anabaena species, Archaeoellipsoides is interpreted as the fossilized remains of akinetes produced by planktic heterocystous cyanobacteria. These fossils set a minimum date for the evolution of derived cyanobacteria capable of marked cell differentiation, and they corroborate geochemical evidence indicating that atmospheric oxygen levels were well above 1% of present day levels 1,500 million years ago.

NASA Discipline Exobiology↗
NASA NTRS1996

Evaluation of Cyanothece sp. ATCC 51142 as a candidate for inclusion in a CELSS

Controlled ecological life support systems (CELSS) have been proposed to make long-duration manned space flights more cost-effective. Higher plants will presumably provide food and a breathable atmosphere for the crew. It has been suggested that imbalances between the CO2/O2 gas exchange ratios of the heterotrophic and autotrophic components of the system will inevitably lead to an unstable system, and the loss of O2 from the atmosphere. Ratio imbalances may be corrected by including a second autotroph with an appropriate CO2/O2 gas exchange ratio. Cyanothece sp. ATCC 51142 is a large unicellular N2-fixing cyanobacterium, exhibiting high growth rates under diverse physiological conditions. A rat-feeding study showed the biomass to be edible. Furthermore, it may have a CO2/O2 gas exchange ratio that theoretically can compensate for ratio imbalances. It is suggested that Cyanothece spp. could fulfill several roles in a CELSS: supplementing atmosphere recycling, generating fixed N from the air, providing a balanced protein supplement, and protecting a CELSS in case of catastrophic crop failure.

Non-NASA Center↗
NASA NTRS1988

The habits of roots: what's up down under?

Defining interactions of roots with the surrounding soil environment has been the focus of many recent investigations. As a result of these efforts, we are gaining an appreciation of the varied and often surprising strategies whereby roots adjust to and condition their soil environment for optimal growth and development. This article summarizes current knowledge of the often complex interactions between roots and biotic and abiotic factors within the soil. These interactions are interpreted in terms of modifications in the development or the physiology of the root.

Review↗
NASA NTRS1981

Rates of fixation by lightning of carbon and nitrogen in possible primitive atmospheres

A thermochemical-hydrodynamic model of the production of trace species by electrical discharges has been used to estimate the rates of fixation of C and N by lightning in the primitive atmosphere. Calculations for various possible mixtures of CH4, CO2, CO, N2, H2, and H2O reveal that the prime species produced were probably HCN and NO and that the key parameter determining the rates of fixation was the ratio of C atoms to O atoms in the atmosphere. Atmospheres with C more abundant than O have large HCN fixation rates, in excess of 10 to the 17th molecules/J, but small NO yields. However, when O is more abundant than C, the NO fixation rate approaches 10 to the 17th molecules/J while the HCN yield is small. The implications for the evolution of life are discussed.

Chameides, W. L.↗
DOE OSTI2024

Ketjenblack-Supported and Unsupported ZrO 2 –ZrN Nanoparticle Systems for Enabling Efficient Electrochemical Nitrogen Reduction to Ammonia

Artificial N 2 fixation via the electrocatalytic nitrogen (N 2 ) reduction reaction (NRR) has been recently promoted as a rational route toward reducing energy consumption and CO 2 emission as compared with the traditional Haber–Bosch process. Nevertheless, optimizing NRR relies on developing highly efficient electrocatalysts. Herein, we report on the reliable and reproducible synthesis of two promising electrocatalysts in either the presence or absence of Ketjenblack (KB), namely, ZrO 2 –ZrN@KB and ZrO 2 –ZrN systems, synthesized through the nitriding of Zr. Both materials had never previously been considered for NRR, to the best of our knowledge. Nevertheless, both of these electrocatalysts incorporated a combination of tetragonal ZrO 2 , ZrON, and cubic ZrN and showed excellent activity and durability toward NH 3 formation. Moreover, the maximum NH3 production rate of 84.1 μg h –1 mg –1 at -0.7 V vs a reversible hydrogen electrode (RHE) was achieved with the ZrO 2 –ZrN electrocatalyst with an impressive Faradaic efficiency of 21.2% at -0.6 V vs RHE, indicating a high selectivity associated with the NRR. Additionally, the catalysts demonstrated excellent stability during the electrolysis process and recycling tests. Here we postulate that the combination of exposed active sites of ZrN and ZrO 2 likely contributes to the enhanced NRR performance attributed to ZrO 2 –ZrN.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Cyanobacterial Biofertilizer Production by Guanidine-Producing Enzymes

Cyanobacterial production of a biofertilizer shows promise as an environmentally benign alternative to conventional nitrogen fertilizers, reducing environmental and energy burdens through light-driven nitrogen and carbon fixation. One route to realizing the potential for a nitrogen-rich, slow-releasing biofertilizer involves the genetic engineering of cyanobacteria to produce guanidine. Recent advances have demonstrated enzymatic guanidine production in cyanobacteria, but an understanding of cyanobacterial guanidine metabolism is still limited. This Perspective highlights strategies and opportunities for cyanobacterial guanidine production in a Design−Build−Test−Learn cycle. Exploring new guanidine-producing enzymes via phylogenetics could expand candidate enzymes, while understanding the metabolism of substrates can identify constraints and opportunities in substrate utilization. Additionally, guanidine sensing and export are crucial areas of study to enable continuous fertilizer production and stable nitrogen flux. These strategies will guide the development of advanced nitrogen biofertilizer strategies for the agricultural sector.

09 BIOMASS FUELS↗
DOE OSTI2021

Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling

Marine nitrogen-fixing microorganisms are an important source of fixed nitrogen in oceanic ecosystems. The colonial cyanobacterium Trichodesmium and diatom symbionts were thought to be the primary contributors to oceanic N 2 fixation until the discovery of the unusual uncultivated symbiotic cyanobacterium UCYN-A ( Candidatus Atelocyanobacterium thalassa ). UCYN-A has atypical metabolic characteristics lacking the oxygen-evolving photosystem II, the tricarboxylic acid cycle, the carbon-fixation enzyme RuBisCo and de novo biosynthetic pathways for a number of amino acids and nucleotides. Therefore, it is obligately symbiotic with its single-celled haptophyte algal host. UCYN-A receives fixed carbon from its host and returns fixed nitrogen, but further insights into this symbiosis are precluded by both UCYN-A and its host being uncultured. In order to investigate how this syntrophy is coordinated, we reconstructed bottom-up genome-scale metabolic models of UCYN-A and its algal partner to explore possible trophic scenarios, focusing on nitrogen fixation and biomass synthesis. Since both partners are uncultivated and only the genome sequence of UCYN-A is available, we used the phylogenetically related Chrysochromulina tobin as a proxy for the host. Through the use of flux balance analysis (FBA), we determined the minimal set of metabolites and biochemical functions that must be shared between the two organisms to ensure viability and growth. We quantitatively investigated the metabolic characteristics that facilitate daytime N 2 fixation in UCYN-A and possible oxygen-scavenging mechanisms needed to create an anaerobic environment to allow nitrogenase to function. This is the first application of an FBA framework to examine the tight metabolic coupling between uncultivated microbes in marine symbiotic communities and provides a roadmap for future efforts focusing on such specialized systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Soil organic matter and plant carbon allocated to nitrogen acquisition simulated by the FUN-BioCROP model

This data package contains the model input, results, and validation data from Juice et al (citation below). The FUN-BioCROP model (Fixation and Uptake of Nitrogen- Bioenergy Carbon, Rhizosphere, Organisms, and Protection) advances the field of bioenergy modeling by integrating new empirical paradigms of the role of belowground processes in shaping coupled carbon (C) and nitrogen (N) cycles. It was developed by modifying the FUN-CORPSE model (Fixation and Uptake of Nitrogen- Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment, Sulman et al. 2017 Ecology Letters) for use in bioenergy systems by including mechanistic tillage, organic matter addition, nitrogen fertilization, harvest, and feedstock-specific parameters, and to be driven by DayCent plant productivity and biomass data.

biofuel sustainability↗
NASA NTRS2016

Nitrogen in Ancient Mud: A Biosignature?

Nitrogen is an essential nutrient for all life on Earth and possibly elsewhere. Burial of nitrogen bound to organic matter constitutes the major flux of nitrogen into sediments today, which has led to the inference that nitrogen enrichments in sedimentary rocks may be a biosignature. However, abiotic processes such as lightning or volcanism can fix atmospheric N2 and contribute to sedimentary nitrogen burial in the absence of life. It is therefore uncertain whether observed nitrogen enrichments of up to 430 ppm in Paleoarchean metasedimentary biotite grains are indeed biogenic. This study seeks to address that problem with a numerical model. The NH4(+) concentration of an abiotic ocean is modeled as a function of source fluxes, pH-dependent NH3 volatilization, and equilibrated adsorption of NH4(+) onto clay particles. The results suggest that the observed nitrogen concentrations in Paleoarchean biotite can only be reconciled with purely abiotic processes if the ocean was more acidic (pH <6) and/or if the source fluxes from lightning and volcanism were at least an order of magnitude higher (≥10(exp 12) mol/yr) than previously thought. The bulk of the nitrogen is thus most likely of biological origin. While this does not necessitate a particular metabolism such as biological N2 fixation, the data provide evidence of nitrogen utilization back to 3.8 Gyr. Nitrogen abundances could thus provide useful information in extraterrestrial missions.

Early Earth↗