Diazotrophic aboveground endophytes in native pines, poplar and willow
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This dataset contains solid-state 13C NMR data and atomistic molecular dynamics simulation files supporting the study of nanoscale secondary cell wall architecture across 13 genetically diverse Populus trichocarpa genotypes grown under uniform greenhouse conditions in 13C-enriched CO2 atmospheres (~89% 13C enrichment).The dataset contains two collections of solid-state 13C NMR data. (1) 200 MHz data (Bruker Avance III HD, 4 mm HX probe, 10 kHz MAS): raw Bruker TopSpin experiment folders and DMFIT-exported ascii spectra for selective and non-selective 1D 13C-13C spin diffusion experiments (3000 ms mixing) used to quantify inter-polymer spatial proximities, and short-mixing (1 ms) reference spectra used for polymeric abundance quantification by spectral deconvolution. (2) 600 MHz data (Bruker Avance III, 1.6 mm PhoenixNMR HXY probe, 30 kHz MAS): raw Bruker TopSpin experiment folders containing 2D CORD, 2D CP-INADEQUATE, and 13C/1H relaxation (T1, T1rho) experiments for all 13 genotypes, with processed Excel workbooks per experiment type. Molecular dynamics simulation code, coordinate files, and analysis scripts (NAMD/CHARMM/Python) for six atomistic cell wall models are included. Summarized ssNMR data are compiled into a single excel file and subjected to statistical analysis. Multivariate analysis code (PCA, Pearson correlation) and summary data are provided as excel worksheets and Jupyter notebooks (Python 3).
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Populus trichocarpa is an important biofuel feedstock that has been the target of extensive research and is emerging as a model organism for plants, especially woody perennials. This research has generated several large ‘omics datasets. However, only few studies in Populus have attempted to integrate various data types. This review will summarize various ‘omics data layers, focusing on their application in Populus species. Subsequently, network and signal processing techniques for the integration and analysis of these data types will be discussed, with particular reference to examples in Populus.
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Here, the biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. In this work we study the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Inoculation individually with either bacterial isolate increased root growth relative to uninoculated controls. Root area, photosynthetic efficiency, gene expression and metabolite expression data in individual and dual inoculated treatments indicate that the effects of these bacteria are unique and additive, suggesting that the function of a microbiome community may be predicted from the additive functions of the individual members.
Investigation of potential tornado-producing thunderstorms was performed during part of the 1972 and 1973 tornado seasons. On May 7, 1973 twenty-one tornadoes were confirmed over southern Missouri, northern Arkansas, and southwestern Illinois. The region was surveyed by high altitude photography performed on a Learjet over the region of reported tornadoes. Two storms were chosen from aircraft observation with the guidance of ground and radar reports, and a series of photographs were taken of a tornado producing cloud. An analysis of the activity before and during the tornado is made, and most noteworthy were changes detected in the growth and collapse of overshooting domes above the anvil. Suggestions are included for a comprehensive study.
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Embodiments of the present invention relate generally to new bioenergy crops and methods of creating new bioenergy crops. For example, genes encoding microRNAs (miRNAs) are used to create transgenic crops. In some embodiments, over-expression of miRNA is used to produce transgenic perennials, such as trees, with altered lignin content or composition. In some embodiments, the transgenic perennials are Populus spp. In some embodiments, the miRNA is a member of the miR156 family. In some embodiments, the gene is Zea mays Cg1.
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Lignin valorization, frequently involving a depolymerization step, is necessary for economic production of lignocellulosic biofuels. However, isolation of lignin frequently degrades the structure such that depolymerization yields from the isolated lignin are decreased relative to the "native" lignin present in the plant. In this work we show that by using flow-through extraction with methanol at 225 degrees C, combined with rapid quenching, we can isolate a "native-like" lignin that produces monomer yields comparable the lignin in the parent biomass under reductive catalytic fractionation (RCF) conditions. This isolated, native-like lignin is shelf-stable at room temperature on a time scale of months, and can be concentrated to a lignin oil and reconstituted in methanol without losing activity. These features will facilitate the study of intrinsic lignin properties and steady-state depolymerization processes.
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Background: Poplars are considered suitable dedicated energy crops, with abundant cellulose and hemicellulose, and huge surplus biomass potential in China. Xylan, the major hemicellulosic component, contributes to the structural stability of wood and represents a tremendous quantity of biobased chemicals for fuel production. Monomeric xylose conversion to value-added chemicals such as furfural, xylitol, and xylonic acid could greatly improve the economics of pulp-paper industry and biorefinery. Acetic acid (HAc) is used as a friendly and recyclable selective catalyst amenable to xylan degradation and xylooligosaccharides production from lignocellulosic materials. However, HAc catalyst usually works much feebly at inert woods than agricultural straws. In this study, effects of different iron species in HAc media on poplar xylan degradation were systematically compared, and a preferable Fe3+-assisted HAc hydrolysis process was proposed for comparable xylose-hydrolysate recovery (XHR) and enzymatic saccharifcation of cellulose. Results: In presence of 6.5% HAc with 0.17–0.25 wt% Fe3+, xylose yield ranged between 72.5 and 73.9%. Additionally, pretreatment was effective in poplar delignification, with a lignin yield falling between 38.6 and 42.5%. Under similar conditions, saccharifcation efficiency varied between 60.3 and 65.9%. Starting with 100 g poplar biomass, a total amount of 12.7–12.8 g of xylose and 18.8–22.8 g of glucose were harvested from liquid streams during the whole process of Fe3+-HAc hydrolysis coupled with enzymatic saccharification. Furthermore, the enhancement mechanism of Fe3+ coupled with HAc was investigated after proof-of-concept experiments. Beechwood xylan and xylose were treated under the same condition as poplar sawdust fractionation, giving understanding of the effect of catalysts on the hydrolysis pathway from wood xylan to xylose and furfural by Fe3+-HAc. Conclusions: The Fe3+-assisted HAc hydrolysis process was demonstrated as an effective approach to the wood xylose and other monosaccharides production. Synergistic effect of Lewis acid site and aqueous acetic acid provided a promising strategy for catalytic valorization of poplar biomass.
Phosphorus is an important plant nutrient, but in soils the majority of phosphorus, present in the form of a phosphate, forms metal complexes in soil making it relatively unavailable to plants. Therefore, inorganic phosphate solubilization is an important process of plant growth promotion by plant associated bacteria and fungi. Non nodulating plant species have been shown to thrive in low-nutrient environments, in some instances by relying on plant associated microorganisms called endophytes. These microorganisms live within the plant and help supply nutrients for the plant. Despite their potential enormous environmental importance, there are a limited number of studies looking at the direct molecular impact of phosphate solubilizing endophytic bacteria on the host plant. In this work, we studied the impact of two endophyte strains of wild poplar (Populus trichocarpa) that solubilize phosphate. Using a combination of x-ray imaging, spectroscopy methods, and proteomics we report direct evidence of endophyte-promoted phosphorus uptake in poplar. We found that the solubilized phosphate inside the plant may react and become insoluble again suggesting that the phosphate could be re-released within the plant by endophytes. Using synchrotron x-ray fluorescence spectromicroscopy combined with x-ray absorption near-edge structure, we visualized the nutrient phosphorus inside poplar roots inoculated by the selected endophytes and found the phosphorus in both forms of organic and inorganic phosphates inside the root. Tomography-based root imaging revealed a markedly different root biomass and root architecture for poplar samples inoculated with the phosphate solubilizing bacteria strains. Proteomics characterization on poplar roots coupled with protein network analysis revealed novel proteins and metabolic pathways with possible involvement in endophyte enriched phosphorus uptake. These findings suggest an important role of endophytes for phosphorus acquisition and provide a deeper understanding of the critical symbiotic associations between poplar and the endophytic bacteria.
This study quantified root biomass distribution; root accrual of C, N, P, and K; and changes in soil organic carbon (SOC) associated with alley-cropped switchgrass (Panicum virgatum L.), prairie cordgrass (Spartina pectinata Bosc ex Link), intermediate wheatgrass [Thinopyrum intermedium (Host) Barkworth and Dewey ‘Rush’], and a native polyculture planted between rows of ‘NM6’ poplar (Populus maximowiczii × P. nigra) and ‘Fish Creek’ willow (Salix purpurea) at two Minnesota sites (Empire and Granada). After 4 yr since establishment, SOC declined at each site but was not influenced by species selection. NM6 poplar–prairie cordgrass systems had among the highest root biomass, C, and nutrient accrual, with up to 16.3 Mg root biomass, 7.0 Mg C, 175 kg N, 31 kg P, and 97 kg K ha -1 . Fine roots were the largest fraction of belowground biomass, although course roots were also a large fraction for poplar and prairie cordgrass. Tree roots extended to 6 m into the crop alley, although 85–89% were within 1 m of tree rows, depending on tree species. Crop fine root biomass was reduced up to 67% at 1 m from tree rows and 20% at 3.5 m and was up to 142% greater in willow than in poplar alleys. Total root C was predominated by poplars at Empire regardless of herbaceous crop type, whereas the proportions of tree and crop root C varied by crop at Granada. These results suggest that prairie cordgrass is well suited to alley cropping and that, due to the competitive ability of poplars, productivity, C sequestration, and nutrient accrual may be greater in willow systems in the long term.