Data from: Plant ammonium sensitivity is associated with the external pH adaptation, repertoire of nitrogen transporters, and nitrogen requirement
Data files
May 24, 2024 version files 360.12 KB
Abstract
Modern crops exhibit diverse sensitivities to ammonium as the primary nitrogen source, influenced by environmental factors such as external pH and nutrient availability. Despite its significance, there is currently no systematic classification of plant species based on their ammonium sensitivity. This study conducts a meta-analysis of 50 plant species and presents a new classification method based on the comparison of fresh biomass obtained under ammonium and nitrate nutrition. The classification uses the natural logarithm of biomass ratio as the size effect indicator of ammonium sensitivity. This numerical parameter is associated with critical factors for nitrogen demand and form preference, such as Ellenberg indicators and the repertoire of nitrogen transporters for ammonium and nitrate uptake. Finally, a comparative analysis of the developmental and metabolic responses, including hormonal balance, is conducted in two species with divergent ammonium sensitivity values in the classification. Results indicate that nitrate has a key counteracting role of ammonium toxicity in species with a higher abundance of genes encoding NRT2-type proteins and fewer of the AMT2-type proteins. Additionally, the study confirms the reliability of the phytohormone balance and methylglyoxal content as indicators for anticipating ammonium toxicity.
README: Rivero-Marcos et al_(2024_JXB)_RAW DATA
https://doi.org/10.5061/dryad.gmsbcc2w6
The Excel data file comprises the raw data for querying, estimating ammonium sensitivity, and replicating the analyses of the following paper: Rivero-Marcos M, Lasa B, Neves T, Zamarreño A.M, García-Mina J.M, García-Olaverri C, Aparicio-Tejo P.M, Cruz C, Ariz A. Plant ammonium sensitivity is associated with the external pH adaptation, repertoire of nitrogen transporters, and nitrogen requirement.
Description of the data and file structure
Each sheet in the Excel file contains the raw data corresponding to the figures in the paper, with methodology described in the Materials & Methods section. In brief:
- Metaanalysis: Fresh weight biomass of shoot, root, and whole plant of species and cultivars grown hydroponically under certain concentrations of nitrate and ammonium, and pH, according to the studies in the metaanalysis, from which LnBR* and its variance were calculated.(*LnBR is defined as the natural logarithm of the ratio between the fresh biomass gained via ammonium or nitrate nutrition. Detail in the M&M section of the manuscript).
- Forest plot_plant_sps: LnBR for plant species under hydroponic conditions for high (≥6.5) and lower (<6.5) external pH. Distinction was made between species included or not in the metaanalysis (based on criteria in table 1 of the main text). Upper and lower limits are shown.
- Forest plot_root_sps: Similar to the previous sheet, but referring to root tissue.
- Forest plot_shoot_sps: Similar to the previous sheet, but referring to shoot tissue.
- Forest plot_plant_cv: Similar to the previous sheet, but here is shown the response to ammonium sensitivity among different cultivars within the same species.
- EIVs: Ellenberg Index Values for each species with information on N (nitrophily), R (pH), and Spread according to 'Italian' and 'British' flora references, 'GBIF' (Global Biodiversity Information Facility), and 'PFAF' (Plant for a Future) databases. The number of members of the NRT1, NRT2, AMT1, and AMT2-onwards gene families per species was shown according to the linked references, or in the 'TAIR', 'Spinach', and 'Pisum Cameor' databases.
- So vs Ps_DW: Fresh weight biomass of root and leaf of two spinach (Winter-Giant) and pea (Sugar-Snap) cultivars according to the nitrogen and external pH regime in hydroponics.
- So_pH 6_ions; Ps_pH 6_ions; So_pH 8_ions; Ps_pH 8_ions: Raw contents of cations and anions in spinach (So) or pea (Ps) cultivar in root and shoot at external pH 6 and 8 according to the nitrogen regime.
- So vs Ps_Hormones: Hormone concentration in spinach and pea cultivars as described in the Excel sheet, for shoot and root under pH 6 and 8 according to the nitrogen regime (N='nitrate'; A='ammonium').
- Phyl_Tree_NRT1s: Amino acid sequence used to construct the phylogenetic tree for identified members of the NRT1/NPF family in Arabidopsis and spinach (species more sensitive to ammonium), and pea and rice (more tolerant).
- Phyl_Tree_NRT2s: Similar to the previous point for members of the NRT2 family.
- Phyl_Tree_AMTs: Similar for the ammonium transporters of the AMT1 and AMT2-onwards families.
In any case, empty cells or cells with the value N/A (not applicable) indicate that no data is available for the specific value in the cited paper (as seen in the meta-analysis sheet).