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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Metabolomic Profiling of Wild-type and Mutant Soybean Root Nodules Using Laser-ablation Electrospray Ionization Mass Spectrometry Reveals Altered Metabolism

The establishment of the nitrogen-fixing symbiosis between soybean and Bradyrhizobium japonicum is complex. In order to document the changes in plant metabolism due to the symbiosis, we utilized laser ablation electrospray ionization mass spectrometry (LAESI-MS) for in situ metabolic profiling of wild-type nodules, nodules infected with a B. japonicum nifH mutant unable to fix nitrogen, nodules doubly infected by both strains, and nodules formed on plants mutated in the stearoyl-acyl carrier protein desaturase (sacpd-c) gene, which were previously shown to have altered nodule ultrastructure. Results showed that the relative abundance of fatty acids, purines, and lipids was significantly changed in response to the symbiosis. The nifH mutant nodules had elevated levels of jasmonic acid (JA), correlating with signs of nitrogen deprivation. Nodules resulting from the mixed inoculant displayed similar, overlapping metabolic distributions within the sectors of effective (fix+) and ineffective (nifH mutant, fix-) endosymbionts. These data are inconsistent with the notion that plant sanctioning is cell autonomous. Nodules lacking sacpd-c displayed an elevation of soyasaponins and organic acids in the central necrotic regions. This study demonstrates the utility of LAESI-MS for high-throughput screening of plant phenotypes. Overall, nodules disrupted in the symbiosis were elevated in metabolites related to plant defense.

Agtuca, Beverly J.↗
NASA NTRS1987

Nodule activity and allocation of photosynthate of soybean during recovery from water stress

Nodulated soybean plants (Glycine max [L.] Merr. cv Ransom) in a growth-chamber study were subjected to a leaf water potential (psi w) of -2.0 megapascal during vegetative growth. Changes in nonstructural carbohydrate contents of leaves, stems, roots, and nodules, allocation of dry matter among plant parts, in situ specific nodule activity, and in situ canopy apparent photosynthetic rate were measured in stressed and nonstressed plants during a 7-day period following rewatering. Leaf and nodule psi w also were determined. At the time of maximum stress, concentration of nonstructural carbohydrates had declined in leaves of stressed, relative to nonstressed, plants, and the concentration of nonstructural carbohydrates had increased in stems, roots, and nodules. Sucrose concentrations in roots and nodules of stressed plants were 1.5 and 3 times greater, respectively, than those of nonstressed plants. Within 12 hours after rewatering, leaf and nodule psi w of stressed plants had returned to values of nonstressed plants. Canopy apparent photosynthesis and specific nodule activity of stressed plants recovered to levels for nonstressed plants within 2 days after rewatering. The elevated sucrose concentrations in roots and nodules of stressed plants also declined rapidly upon rehydration. The increase in sucrose concentration in nodules, as well as the increase of carbohydrates in roots and stems, during water stress and the rapid disappearance upon rewatering indicates that inhibition of carbohydrate utilization within the nodule may be associated with loss of nodule activity. Availability of carbohydrates within the nodules and from photosynthetic activity following rehydration of nodules may mediate the rate of recovery of N2-fixation activity.

Non-NASA Center↗
DOE OSTI2020

Mineralogical transformations in polymetallic nodules and the change of Ni, Cu and Co crystal-chemistry upon burial in sediments

Polymetallic nodules from the Clarion and Clipperton Zone of the equatorial Pacific Ocean were studied using X-ray diffraction, X-ray absorption, Fourier-transformed infrared spectroscopy and transmission electron microscopy. Here, this study includes nodules found at the sediment surface as well as subsurface (14–16 cm sediment depth) and deeply buried (530–985 cm sediment depth) nodules. The surface and subsurface nodules are currently under oxic conditions whereas the deeply buried nodules are under suboxic conditions. Surface nodules consist mainly of turbostratic phyllomanganates (7 Å and 10 Å vernadite and Fe-vernadite); todorokite is a minor phase, if present at all. In contrast, subsurface and especially deeply buried nodules predominantly consist of todorokite, which increases in abundance with depth in the sediment. Thus, upon burial of nodules within the shallow sediment, phyllomanganates transform to todorokite, probably through the combined action of time and change in the ambient chemical conditions. Nodules from deeper sediment depth (>500 cm) consist primarily of todorokite and additionally show signs of dissolution. The transformation of phyllomanganates to todorokite and their further dissolution upon nodule burial under suboxic conditions induces modifications in the crystal-chemistry of Ni, Co, and Cu. In surface nodules, Ni and Co are incorporated in the octahedral sheets of phyllomanganates, whereas Cu mainly is located at the edges of those phyllomanganate sheets. In buried nodules Cu and to a lesser extent Ni are incorporated in todorokite by forming outer-sphere complexes within the tunnels. However, Ni is predominantly incorporated within the octahedra of the newly formed todorokite structure. Co is also enriched in the octahedra of todorokite as a result of dissolution of hydrogenetic vernadite and re-incorporation in the more stable Mn-phase formed during the diagenetic transformation. Co enrichment under suboxic conditions after burial within the sediments is noteworthy since Co in surface nodules is characteristic for oxic conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Spatiotemporal cytokinin response imaging and ISOPENTENYLTRANSFERASE 3 function in Medicago nodule development

Most legumes can establish a symbiotic association with soil rhizobia that trigger the development of root nodules. These nodules host the rhizobia and allow them to fix nitrogen efficiently. The perception of bacterial lipo-chitooligosaccharides (LCOs) in the epidermis initiates a signaling cascade that allows rhizobial intracellular infection in the root and de-differentiation and activation of cell division that gives rise to the nodule. Thus, nodule organogenesis and rhizobial infection need to be coupled in space and time for successful nodulation. The plant hormone cytokinin (CK) contributes to the coordination of this process, acting as an essential positive regulator of nodule organogenesis. However, the temporal regulation of tissue-specific CK signaling and biosynthesis in response to LCOs or Sinorhizobium meliloti inoculation in Medicago truncatula remains poorly understood. In this study, using a fluorescence-based CK sensor (pTCSn::nls:tGFP), we performed a high-resolution tissue-specific temporal characterization of the sequential activation of CK response during root infection and nodule development in M. truncatula after inoculation with S. meliloti. Loss-of-function mutants of the CK-biosynthetic gene ISOPENTENYLTRANSFERASE 3 (IPT3) showed impairment of nodulation, suggesting that IPT3 is required for nodule development in M. truncatula. Simultaneous live imaging of pIPT3::nls:tdTOMATO and the CK sensor showed that IPT3 induction in the pericycle at the base of nodule primordium contributes to CK biosynthesis, which in turn promotes expression of positive regulators of nodule organogenesis in M. truncatula.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The soybean β‐expansin gene GmINS1 contributes to nodule development in response to phosphate starvation

Abstract Legume biological nitrogen fixation (BNF) is the most important N source in agricultural ecosystems. Nodule organogenesis from the primordia to the development of mature nodules with the ability to fix N 2 largely determines BNF capacity. However, nodule growth is often limited by low phosphorus (P) availability, while the mechanisms underlying nodule development responses to P deficiency remain largely unknown. In this study, we found that nodule enlargement is severely inhibited by P deficiency, as reflected by the smaller individual nodule size from a soybean core collection in the field. Wide‐ranging natural diversity in nodule size was further identified in soybeans reared in low P soils, with the FC‐1 genotype outperforming FC‐2 in assessments of nodulation under low P conditions. Among β‐expansin members, GmINS1 expression is most abundantly enhanced by P deficiency in FC‐1 nodules, and its transcript level is further displayed to be tightly associated with nodule enlargement. Four single nucleotide polymorphisms discovered in the GmINS1 promoter distinguished the FC‐1 and FC‐2 genotypes and accounted for the differential expression levels of GmINS1 responses to P deficiency. GmINS1 overexpression led to increases in nodule size, infected cell abundance, and N 2 fixation capacity and subsequently promoted increases in N and P content, soybean biomass, and yield. Our findings provide a candidate gene for optimizing BNF capacity responses to low P stress in soybean molecular breeding programs.

Yang, Zhaojun↗
NASA NTRS1992

Stimulation of nodulation in field peas (Pisum sativum) by low concentrations of ammonium in hydroponic culture

Although the inhibitory effects of high concentrations of mineral N (> 1.0 mM) on nodule development and function have often been studied, the effects of low, static concentrations of NH4+ (< 1.0 mM) on nodulation are unknown. In the present experiments we examine the effects of static concentrations of NH4+ at 0, 0.1 and 0.5 mM in flowing, hydroponic culture on nodule establishment and nitrogenase activity in field peas [Pisum sativum L. cv. Express (Svalof AB)] for the initial 28 days after planting (DAP). Peas grown in the presence of low concentrations of NH4+ had significantly greater nodule numbers (up to 4-fold) than plants grown without NH4+. Nodule dry weight per plant was significantly higher at 14, 21 and 28 DAP in plants grown in the presence of NH4+, but individual nodule mass was lower than in plants grown without NH4+. The nodulation pattern of the plants supplied with NH4+ was similar to that often reported for supernodulating mutants, however the plants did not express other growth habits associated with supernodulation. Estimates of N2 fixation indicate that the plus-NH4+ peas fixed as much or more N2 than the plants supplied with minus-NH4+ nutrient solution. There were no significant differences in nodule numbers, nodule mass or NH4+ uptake between the plants grown at the two concentrations of NH4+. Nodulation appeared to autoregulate by 14 DAP in the minus-NH4+ treatment. Plant growth and N accumulation in the minus-NH4+ plants lagged behind those of the plus-NH4+ treatments prior to N2 fixation becoming well established in the final week of the experiment. The plus-NH4+ treatments appeared not to elicit autoregulation and plants continued to initiate nodules throughout the experiment.

NASA Program CELSS↗
DOE OSTI2026

Synchrotron resolved microscale mineralogy and elemental composition of individual plinthic and manganiferous nodules from agricultural soils

Iron and manganese oxides are strong sorbents and elemental scavengers in the environment that can form macroscopic nodules in soils. Despite their importance in the geochemical cycling of nutrients and contaminants, nodules are rarely characterized. When analyzed, they are often combined into bulk samples, obscuring individual characteristics. This study investigates the composition and mineralogy of individual plinthic and manganiferous nodules in soil from cropping systems in the Farming Systems Project in Beltsville, Maryland. Elemental composition indicates the accumulation of contaminants and nutrients, including copper in all nodules and high levels of phosphorus in select nodules. Sequential extractions determine that highly crystalline minerals comprise the nodules, locking away these nutrients and contaminants. Bulk X-ray diffraction (XRD) demonstrated distinct mineralogies in the plinthic and manganiferous nodules, with the former comprised of quartz, goethite, and kaolinite, and the latter consisting of quartz, Mn 2 O 3 , and hematite. Synchrotron and laboratory-based X-ray fluorescence (XRF) mapping gives critical insight into the elemental distribution within the nodules and elucidates spatial elemental associations, including the coupling of manganese and iron in the manganiferous nodules. XRF maps paired with µXRD provide microscale spatial resolution in mineralogy, which resolved several phases not apparent in bulk XRD, manganese’s association with goethite, and minerals indicative of redox transformations, including magnetite and maghemite. These novel results provide critical insight into the microscale mineralogy and individual elemental composition of plinthic and manganiferous nodules, as well as how they alter bulk soil geochemistry in ways largely unaccounted for in research on soil systems.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Genetic variation and genetic complexity of nodule occupancy in soybean inoculated with USDA110 and USDA123 rhizobium strains

Abstract Background Symbiotic nitrogen fixation differs among Bradyrhizobium japonicum strains. Soybean inoculated with USDA123 has a lower yield than strains known to have high nitrogen fixation efficiency, such as USDA110. In the main soybean-producing area in the Midwest of the United States, USDA123 has a high nodule incidence in field-grown soybean and is competitive but inefficient in nitrogen fixation. In this study, a high-throughput system was developed to characterize nodule number among 1,321 Glycine max and 69 Glycine soja accessions single inoculated with USDA110 and USDA123. Results Seventy-three G. max accessions with significantly different nodule number of USDA110 and USDA123 were identified. After double inoculating 35 of the 73 accessions, it was observed that PI189939, PI317335, PI324187B, PI548461, PI562373, and PI628961 were occupied by USDA110 and double-strain nodules but not by USDA123 nodules alone. PI567624 was only occupied by USDA110 nodules, and PI507429 restricted all strains. Analysis showed that 35 loci were associated with nodule number in G. max when inoculated with strain USDA110 and 35 loci with USDA123. Twenty-three loci were identified in G. soja when inoculated with strain USDA110 and 34 with USDA123. Only four loci were common across two treatments, and each locus could only explain 0.8 to 1.5% of phenotypic variation. Conclusions High-throughput phenotyping systems to characterize nodule number and occupancy were developed, and soybean germplasm restricting rhizobium strain USDA123 but preferring USDA110 was identified. The larger number of minor effects and a small few common loci controlling the nodule number indicated trait genetic complexity and strain-dependent nodulation restriction. The information from the present study will add to the development of cultivars that limit USDA123, thereby increasing nitrogen fixation efficiency and productivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Viruses of Nitrogen-Fixing Mesorhizobium Bacteria in Globally Distributed Chickpea Root Nodules

Legume nodules are specialized environments on plant roots that are induced and dominated by nitrogen-fixing bacteria. Bacteriophages (phages) in these nodules could potentially provide top-down controls on the population size and, therefore, the function of nitrogen-fixing symbionts. Here we sought to characterize the diversity and biogeographical patterns of phages that infect nitrogen-fixing Mesorhizobium symbionts isolated from root nodules, leveraging 266 genomes of Mesorhizobium isolated from nodules and 648 nodule metagenomes collected from three species of chickpea plants ( Cicer spp.) under different agricultural management practices, spanning eight countries on five continents. We identified 106 phage populations (viral operational taxonomic units [vOTUs]) in Mesorhizobium draft genomes, 37% of which were confirmed as likely prophages. These vOTUs were detected in 64% of the Mesorhizobium-dominated nodule metagenomes and 58% of the Mesorhizobium isolates. Per metagenome, 1 to 16 putative Mesorhizobium vOTUs were detected, with more than half of the nodules containing only one such vOTU. The majority of vOTUs were detected exclusively in Ethiopia, followed by India and Morocco, with the lowest richness of putative Mesorhizobium phages in countries that applied industrial Mesorhizobium inoculants to crops. Two vOTUs were identified in five or more countries and in nodules dominated by different strains of Mesorhizobium, suggesting infection of diverse Mesorhizobium hosts and long-term interactions. Beta-diversity of these Mesorhizobium phage assemblages was significantly correlated with the dominant Mesorhizobium strain, but not with measured environmental parameters. Our findings indicate that nitrogen-fixing nodules in chickpea plants can contain distinct viral assemblages, with potential impacts on the nodule microbiome that bear further exploration.

Microbiology↗
DOE OSTI2020

Feature‐shared adaptive‐boost deep learning for invasiveness classification of pulmonary subsolid nodules in CT images

Purpose In clinical practice, invasiveness is an important reference indicator for differentiating the malignant degree of subsolid pulmonary nodules. These nodules can be classified as atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), or invasive adenocarcinoma (IAC). The automatic determination of a nodule's invasiveness based on chest CT scans can guide treatment planning. However, it is challenging, owing to the insufficiency of training data and their interclass similarity and intraclass variation. To address these challenges, we propose a two‐stage deep learning strategy for this task: prior‐feature learning followed by adaptive‐boost deep learning. Methods The adaptive‐boost deep learning is proposed to train a strong classifier for invasiveness classification of subsolid nodules in chest CT images, using multiple 3D convolutional neural network (CNN)‐based weak classifiers. Because ensembles of multiple deep 3D CNN models have a huge number of parameters and require large computing resources along with more training and testing time, the prior‐feature learning is proposed to reduce the computations by sharing the CNN layers between all weak classifiers. Using this strategy, all weak classifiers can be integrated into a single network. Results Tenfold cross validation of binary classification was conducted on a total of 1357 nodules, including 765 noninvasive (AAH and AIS) and 592 invasive nodules (MIA and IAC). Ablation experimental results indicated that the proposed binary classifier achieved an accuracy of with an AUC of 81.3 . These results are superior compared to those achieved by three experienced chest imaging specialists who achieved an accuracy of , , and , respectively. About 200 additional nodules were also collected. These nodules covered 50 cases for each category (AAH, AIS, MIA, and IAC, respectively). Both binary and multiple classifications were performed on these data and the results demonstrated that the proposed method definitely achieves better performance than the performance achieved by nonensemble deep learning methods. Conclusions It can be concluded that the proposed adaptive‐boost deep learning can significantly improve the performance of invasiveness classification of pulmonary subsolid nodules in CT images, while the prior‐feature learning can significantly reduce the total size of deep models. The promising results on clinical data show that the trained models can be used as an effective lung cancer screening tool in hospitals. Moreover, the proposed strategy can be easily extended to other similar classification tasks in 3D medical images.

Wang, Jun↗
DOE OSTI2020

Impact of Soil Salinity on the Cowpea Nodule-Microbiome and the Isolation of Halotolerant PGPR Strains to Promote Plant Growth under Salinity Stress

Cowpea is one of the major legumes cultivated in arid and semiarid regions of the world. Four soil-microbial samples (SS-1 through SS-4) collected from semiarid soils in Punjab, Pakistan were planted with cowpea (Vigna unguiculata) crops, which were grown under salinity stress to analyze bacterial composition in the rhizosphere and within nodules using cultivation-dependent and -independent methods. Two varieties, 603 and the salt-tolerant CB 46, were each inoculated with or without the four different native soil samples or grown in medium either N-deficient (-N) or supplemented with N (+N). Plants inoculated with soil samples SS-2 and SS-4 grew better than plants inoculated with SS-1- and SS-3 and grew comparably with the +N controls. Environmental DNA (eDNA) was isolated from SS-1 and SS-4, and, by 16S ribosomal RNA sequencing, the soil microbiomes consisted mainly of Actinobacteria, Firmicutes, Proteobacteria, and other nonproteobacterial genera. However, analysis of eDNA isolated from cowpea nodules established by the trap plants showed that the nodule microbiome consisted almost exclusively of proteobacterial sequences, particularly species of Bradyrhizobium. Bacteria were isolated from both soils and nodules, and 34 of the 51 isolates tested positive for plant-growth-promoting rhizobacteria traits in plate assays. Many could serve as future inocula for crops in arid soils. The discrepancy between the types of bacteria isolated by culturing bacteria isolated from surface-sterilized cowpea nodules (proteobacteria and nonproteobacteria) versus those detected by sequencing DNA isolated from the nodules (proteobacteria) from cowpea nodules (proteobacteria and nonproteobacteria) versus those detected in the nodule microbiome (proteobacteria) needs further study.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2018

Enigmatic Nodule-Bearing Rocks in the Mafic to Ultramafic Diana Mills Pluton, Piedmont Province, Virginia

The Silurian Diana Mills pluton is a metamorphosed mafic-ultramafic body in the Piedmont Province of Virginia. Major rock types in the pluton include metadiorite and chlorite‐amphibole rock, with lesser amounts of hornblendite. However, the most visually striking rocks, found at 4 locations, consist of tan‐weathering nodules in a dark green matrix. The purpose of this study was to investigate the origin of these nodular rocks. All rocks show evidence of greenschistfacies metamorphism, but relict igneous textures are preserved locally. Apart from the nodules, Ca‐amphibole is ubiquitous in all rock types. Nodules are dominated by serpentine or talc (+magnetite +/- chromite), and many show a thin (less than or equal to 5 mm) radially oriented shell of serpentine against adjacent matrix. The nodules are ultramafic (Mg# approx. 80-90, up to7,563 ppm Cr, up to 2,038 ppm Ni), and their normative mineralogy is dominated by olivine and orthopyroxene. Thus, they represent metamorphosed harzburgites and pyroxenites. Matrix minerals are dominantly amphibole + chlorite, along with variable amounts of talc + magnetite. Some matrix samples are chlorite‐rich, probably reflecting metasomatic reaction with nodules (i.e., they are small‐scale ''blackwalls''). Matrix samples are also ultramafic (high Mg#, Cr, and Ni). The matrix of the nodule‐bearing outcrops is essentially the same as other chlorite‐amphibole rocks elsewhere in the pluton. We consider these rocks to represent emplacement of an original hornblende peridotite crystal mush (a mixture of crystals and hydrous melt), which locally carried harzburgitic nodules. The nodules most likely represent the earliest‐formed cumulates from the Diana Mills parent magma.

Owens, Brent E.↗
DOE OSTI2021

Influence of PRE-emergence herbicides on soybean development, root nodulation and symbiotic nitrogen fixation

We report widespread occurrence of herbicide-resistant weeds has further limited effective POST-emergence herbicide options in soybean (Glycine max (L.) Merr.) leading to an increased adoption of PRE-emergence herbicides. The objective of this study was to investigate the influence of 11 commonly used PRE herbicides on soybean development, root nodulation, and symbiotic N fixation. Soybean plants were grown under greenhouse conditions in pots (10 L; 4 plants per pot) filled with silt loam soil and treated one day after planting with a labeled field rate of imazethapyr, chlorimuron-ethyl, cloransulam-methyl, metribuzin, sulfentrazone, flumioxazin, saflufenacil, acetochlor, S-metolachlor, dimethenamid-P, pyroxasulfone and no herbicide (nontreated control). Sulfentrazone reduced soybean canopy at the VC growth stage but no canopy reduction was observed at the V2 growth stage from any of the herbicide treatments. At the R2 growth stage, herbicides had no effect on soybean development (root and shoot biomass), root nodulation (# nodule per plant, nodule diameter, and nodule biomass) and symbiotic N fixation (acetylene reduction assay and 15 N natural abundance). According to our findings, although PRE herbicides may slightly affect early-season soybean development, the impacts on plant growth, root nodulation, and symbiotic N fixation were negligible. Thus, when sprayed according to the label, the benefits of PRE herbicides for weed control likely outweigh any potential concern regarding soybean development, root nodulation, and N fixation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Partners in root nodule symbiosis respond uniquely to heavy metal stresses in a host genotype-dependent manner

Abstract The mutualistic symbiosis between legume roots and soil rhizobia culminates in the formation of root nodules, where nitrogen is fixed. Root nodule symbiosis is inhibited by heavy metal stress. In this study, we investigated the relative responses of the symbiotic partners to a non-essential heavy metal cadmium (Cd) and an essential heavy metal zinc (Zn) stress and identified patterns in gene expression. We performed dual transcriptomics in nodules, using theMedicago truncatula-Sinorhizobium melilotisymbiotic system. Phenotypes were measured in the wild-typeMedicago truncatulaand a mutant in anABCtransporter gene (Mtabcg36), which showed compromised nodule formation in control conditions and further after heavy metal treatment. We observed that the rhizobia were particularly sensitive to Zn in mutant nodules. The greatest degree of differential gene expression in the host plant were observed under Cd and Zn treatments in wild-type nodules. Most Cd-regulated host genes were also differentially regulated by Zn, revealing little discernment between an essential and a non-essential ion under increased exposure. Furthermore, the host response to both the stresses affected auxin and iron homeostasis genes in a host genotype-dependent manner. Our results suggested impaired cadmium export from the mutant nodules. These results have potential implications in agricultural management systems and bioremediation strategies.

Science & Technology - Other Topics↗
DOE OSTI2024

The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.

Cell Biology↗
NASA NTRS1986

Composition and formation of metal nodules and veins in ordinary chondrites

Five large metal nodules, a composite sample of five small metal nodules, one troilite nodule, and two metal veins from five ordinary chondrites were analyzed by electron microprobe and neutron activation analysis. Metal nodules and veins in H chondrites generally consist of large single crystals of kamacite, whereas L nodules contain significant taenite. Most nodules and veins are depleted by large factors ranging up to 240 in refractory siderophiles (Re, Os, Ir, Pt). Tungsten (normally a refractory siderophile) and Au, As, and Ga (volatile siderophiles) have abundance ratios similar to those of the common siderophiles Fe, Co and Ni. It is proposed that the metal with extremely low refractory-element contents was produced by shock-induced vaporization of chondritic material. The refractory elements condensed near the point of vaporization and were not transported with the vapor. Because the shock-generated gas was mildly oxidizing, W formed volatile oxides.

Widom, E.↗
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

Mercury-Tolerant Ensifer medicae Strains Display High Mercuric Reductase Activity and a Protective Effect on Nitrogen Fixation in Medicago truncatula Nodules Under Mercury Stress

Mercury (Hg) is extremely toxic for all living organisms. Hg-tolerant symbiotic rhizobia have the potential to increase legume tolerance, and to our knowledge, the mechanisms underlying Hg tolerance in rhizobia have not been investigated to date. Rhizobial strains of Ensifer medicae, Rhizobium leguminosarum bv. trifolii and Bradyrhizobium canariense previously isolated from severely Hg-contaminated soils showed different levels of Hg tolerance. The ability of the strains to reduce mercury Hg 2+ to Hg o , a volatile and less toxic form of mercury, was assessed using a Hg volatilization assay. In general, tolerant strains displayed high mercuric reductase activity, which appeared to be inducible in some strains when grown at a sub-lethal HgCl 2 concentration. A strong correlation between Hg tolerance and mercuric reductase activity was observed for E. medicae strains, whereas this was not the case for the B. canariense strains, suggesting that additional Hg tolerance mechanisms could be playing a role in B. canariense. Transcript abundance from merA, the gene that encodes mercuric reductase, was quantified in tolerant and sensitive E. medicae and R. leguminosarum strains. Tolerant strains presented higher merA expression than sensitive ones, and an increase in transcript abundance was observed for some strains when bacteria were grown in the presence of a sub-lethal HgCl 2 concentration. These results suggest a regulation of mercuric reductase in rhizobia. Expression of merA genes and mercuric reductase activity were confirmed in Medicago truncatula nodules formed by a sensitive or a tolerant E. medicae strain. Transcript accumulation in nodules formed by the tolerant strain increased when Hg stress was applied, while a significant decrease in expression occurred upon stress application in nodules formed by the Hg-sensitive strain. The effect of Hg stress on nitrogen fixation was evaluated, and in our experimental conditions, nitrogenase activity was not affected in nodules formed by the tolerant strain, while a significant decrease in activity was observed in nodules elicited by the Hg-sensitive bacteria. Our results suggest that the combination of tolerant legumes with tolerant rhizobia constitutes a potentially powerful tool in the bioremediation of Hg-contaminated soils.

59 BASIC BIOLOGICAL SCIENCES↗