DOI: 10.5061/dryad.cnp5hqc9s
title: Data from: Nitrogen fixation and fertilization have similar effects on biomass allocation in nitrogen-fixing plants

description: Plants adjust their allocation to different organs based on nutrient
 supply. In some plant species, symbioses with nitrogen-fixing bacteria
 that live in root nodules provide an alternate pathway for nitrogen
 acquisition. Does access to nitrogen-fixing bacteria modify plants’
 biomass allocation? We hypothesized that access to nitrogen-fixing
 bacteria would have the same effect on allocation to aboveground versus
 belowground tissues as access to plentiful soil nitrogen. To test this
 hypothesis and related hypotheses about allocation to stems versus leaves
 and roots versus nodules, we conducted experiments with 15 species of
 nitrogen-fixing plants in two separate greenhouses. In each, we grew
 seedlings with and without access to symbiotic bacteria across a wide
 gradient of soil nitrogen supply. As is common, uninoculated plants
 allocated relatively less biomass belowground when they had more soil
 nitrogen. As we hypothesized, nitrogen fixation had a similar effect as
 the highest level of fertilization on allocation aboveground versus
 belowground. Both nitrogen fixation and high fertilization led to ~10%
 less biomass allocated belowground (~10% more aboveground) than the
 uninoculated, lowest fertilization treatment. Fertilization reduced
 allocation to nodules relative to roots. The responses for allocation of
 aboveground tissues to leaves versus stems were not as consistent across
 greenhouses or species as the other allocation trends, though more
 nitrogen fixation consistently led to relatively more allocation to leaves
 when soil nitrogen supply was low. Synthesis: Our results suggest that
 symbiotic nitrogen fixation causes seedlings to allocate relatively less
 biomass belowground, with potential implications for competition and
 carbon storage in early forest development.
description: # Data from: Nitrogen fixation and fertilization have similar effects on
 biomass allocation in nitrogen-fixing plants
 [https://doi.org/10.5061/dryad.cnp5hqc9s](https://doi.org/10.5061/dryad.cnp5hqc9s) ## Description of the data and file structure Reference information: Dataset title: Data for the article "Nitrogen fixation and fertilization have similar effects on biomass allocation in nitrogen-fixing plants," accepted in 2024 by Ecology and Evolution. Dataset contributors: Duncan N. L. Menge, Amelia A. Wolf, Jennifer L. Funk, Steven S. Perakis, ``` K. A. Carreras Pereira ``` Version number 1.0.0 Date: July 21, 2023 Dataset DOI: XXXDOIXXX Suggested citations: ``` Dataset citation: Menge DNL, Wolf AA, Funk JL, Perakis SS, Carreras Pereira KA. 2023. Data for the article "Nitrogen fixation and fertilization have similar effects on biomass allocation in nitrogen-fixing plants", Dryad, Dataset, XXXDOIXXX Corresponding publication: Menge DNL, Wolf AA, Funk JL, Perakis SS, Carreras Pereira KA. 2024. Nitrogen fixation and fertilization have similar effects on biomass allocation in nitrogen-fixing plants. Ecology and Evolution, accepted. ``` Contact information: ``` Duncan Menge Department of Ecology, Evolution, and Environmental Biology, Columbia University dm2972@columbia.edu ORCID ID: 0000-0003-4736-9844 ``` Funding sources: ``` National Science Foundation DEB-1457650 (DNLM, SSP) National Science Foundation DEB-1457444 (JLF) National Science Foundation IOS-2129542 (DNLM) ``` Dates and locations of data collection: ``` Dates: Greenhouse data were collected between 2016 and September 2018 Locations: Greenhouse data were collected from greenhouses in New York, New York and Davis, California. ``` ### Files and variables Data and code file details: In this section we describe (1) the data file, (2) the code files, and (3) the relationship between the code and the data. 1\. Data file General description: This is the only datafile for this paper. Variables: ``` Counter: Row counter. Allowable values: natural numbers. Species: Four-letter code for species. Allowable values: ACFA, ACKO, ALAC, ALJU, ALRU, ALTE, CAEQ, ELAN, ENCY, GLMA, GLSE, LELE, MOCE, MOFA, ROPS, SOCH Note that not all species in the data file were used for this analysis, as some did not nodulate. TRT: Inoculation treatment. Allowable values: plus, minus. N: Fertilization treatment. Allowable values: 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 9.5, 10, 10.5, 11, 9P, 10.5P, 11P These were internal codes used that correspond to the addition rates of N and P. The actual rates are shown in the columns described below. Higher numbers mean higher N addition rates. "P" means a high P treatment. Rep: Replicate. Allowable values: a, b, c Nadded_gN_m2_yr: N fertilization rate in g N/m^2 pot/y. Allowable values: Decimal values ranging from 0.3 to 75. Nadded_mg_per_fert: N fertilization level in mg N per fertilization event. Allowable values: Decimal values ranging from about 0.1 to about 29. Padded_gP_m2_yr: P fertilization rate in g P/m^2 pot/y. Allowable values: 0.17, 0.34, 15. Padded_mg_per_fert: P fertilization level in mg P per fertilization event. Allowable values: Decimal values corresponding to the g P/m^2 pot/yr levels. Location: Barnard or Davis. Leaves_mg: Dry mass in mg of leaf tissue that was on the plant at harvest time. Allowable values: non-negative decimal values, NA. Stem_mg: Dry mass in mg of stem tissue that was on the plant at harvest time. Allowable values: non-negative decimal values, NA. Root_mg: Dry mass in mg of root tissue that was on the plant at harvest time. Allowable values: non-negative decimal values, NA. Nodule_mg: Dry mass in mg of nodule tissue that was on the plant at harvest time. Allowable values: non-negative decimal values, NA. Licor_leaf_mg: Dry mass in mg of leaves used for Licor measurements prior to harvest. Allowable values: non-negative decimal values, NA. Thorn_mg: Dry mass in mg of thorn tissue that was on the plant at harvest time. Only relevant for ACFA and ROPS. Allowable values: non-negative decimal values, NA. Extra_leaf_mg: Dry mass in mg of leaf tissue that had fallen prior to harvest. Allowable values: non-negative decimal values, NA. Length_mm: Length in mm of the main stem of the plant at harvest time. Allowable values: non-negative decimal values, NA. Stem_diameter_mm: Diameter in mm of the stem at the ground at harvest time. Allowable values: non-negative decimal values, NA. Nodules_pink: Whether or not nodules were pink inside. Only checked for a few individuals. Allowable values: Y, N, NA Seed_mass_meanof20wseeds: Arithmetic mean mass in mg of 20 seeds from this species (not individual-specific). Allowable values: Non-negative decimal values, NA. Seed_mass_sdof20seeds: Standard deviation of mass in mg of 20 seeds from this species (not individual-specific). Allowable values: Non-negative decimal values, NA. Seed_percentN: Assumed % N of seeds, based on prior measurements. Allowable measurements: Non-negative decimal values, NA. InoculationDate: Date of inoculation. Allowable values: Date, NA. FertilizationStartDate: Date of first fertilization. Allowable values: Date, NA. FertilizationEndDate: Date of last fertilization. Allowable values: Date, NA. Fertilizations: Number of fertilizations. Allowable values: natural numbers, NA. DateReplaced: Date this individual was replaced. Allowable values: Date, NA. HarvestDate: Date of harvest. Allowable values: Date, NA. Harvest_date_on_envelope: Date listed on the harvest envelope, which sometimes differed from the actual harvest date for a variety of reasons. Allowable values: Date, NA. Days: Number of days of growth under experimental treatments. Allowable values: natural numbers, NA. AP15N_combined: Atom % 15N of combined (leaves, stem, root, and nodule all together) tissue. Allowable values: Non-negative decimal values, NA. d15N_combined: delta 15N of combined tissues. Allowable values: Decimal values, NA. N_cg_g_combined: N content in centigrams per gram (aka %) of combined tissues. Allowable values: Non-negative decimal values, NA. AP13C_combined: Atom % 13C of combined tissues. Allowable values: Non-negative decimal values, NA. d13C_combined: delta 13C of combined tissues. Allowable values: Decimal values, NA. C_cg_g_combined: C content in cg/g of combined tissues. Allowable values: Non-negative decimal values, NA. AP15N_leaves: Atom % 15N of leaf tissue. Allowable values: Non-negative decimal values, NA. d15N_leaves: delta 15N of leaf tissues. Allowable values: Decimal values, NA. N_cg_g_leaves: N content in centigrams per gram (aka %) of leaf tissues. Allowable values: Non-negative decimal values, NA. AP13C_leaves: Atom % 13C of leaf tissues. Allowable values: Non-negative decimal values, NA. d13C_leaves: delta 13C of leaf tissues. Allowable values: Decimal values, NA. C_cg_g_leaves: C content in cg/g of leaf tissues. Allowable values: Non-negative decimal values, NA. AP15N_stem: Atom % 15N of stem tissue. Allowable values: Non-negative decimal values, NA. d15N_stem: delta 15N of stem tissues. Allowable values: Decimal values, NA. N_cg_g_stem: N content in centigrams per gram (aka %) of stem tissues. Allowable values: Non-negative decimal values, NA. AP13C_stem: Atom % 13C of stem tissues. Allowable values: Non-negative decimal values, NA. d13C_stem: delta 13C of stem tissues. Allowable values: Decimal values, NA. C_cg_g_stem: C content in cg/g of stem tissues. Allowable values: Non-negative decimal values, NA. AP15N_root: Atom % 15N of root tissue. Allowable values: Non-negative decimal values, NA. d15N_root: delta 15N of root tissues. Allowable values: Decimal values, NA. N_cg_g_root: N content in centigrams per gram (aka %) of root tissues. Allowable values: Non-negative decimal values, NA. AP13C_root: Atom % 13C of root tissues. Allowable values: Non-negative decimal values, NA. d13C_root: delta 13C of root tissues. Allowable values: Decimal values, NA. C_cg_g_root: C content in cg/g of root tissues. Allowable values: Non-negative decimal values, NA. AP15N_nodule: Atom % 15N of nodule tissue. Allowable values: Non-negative decimal values, NA. d15N_nodule: delta 15N of nodule tissues. Allowable values: Decimal values, NA. N_cg_g_nodule: N content in centigrams per gram (aka %) of nodule tissues. Allowable values: Non-negative decimal values, NA. AP13C_nodule: Atom % 13C of nodule tissues. Allowable values: Non-negative decimal values, NA. d13C_nodule: delta 13C of nodule tissues. Allowable values: Decimal values, NA. C_cg_g_nodule: C content in cg/g of nodule tissues. Allowable values: Non-negative decimal values, NA. N_cg_g_licor: N content in centigrams per gram (aka %) of leaves used for Licor measurements. Allowable values: Non-negative decimal values, NA. C_cg_g_licor: C content in centigrams per gram (aka %) of leaves used for Licor measurements. Allowable values: Non-negative decimal values, NA. N_cg_g_extra: N content in centigrams per gram (aka %) of extra leaves. Allowable values: Non-negative decimal values, NA. C_cg_g_extra: C content in centigrams per gram (aka %) of extra leaves. Allowable values: Non-negative decimal values, NA. Notes: Free-form column for notes. Allowable values: Text string, empty, NA N_cg_g_stem_ChapmanLab: N content in cg/g of stem tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. C_cg_g_stem_ChapmanLab: C content in cg/g of stem tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. N_cg_g_root_ChapmanLab: N content in cg/g of root tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. C_cg_g_root_ChapmanLab: C content in cg/g of root tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. N_cg_g_nodule_ChapmanLab: N content in cg/g of nodule tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. C_cg_g_nodule_ChapmanLab: C content in cg/g of nodule tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. N_cg_g_licor_ChapmanLab: N content in cg/g of Licor leaf tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. C_cg_g_licor_ChapmanLab: C content in cg/g of Licor leaf tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. N_cg_g_extra_ChapmanLab: N content in cg/g of extra leaf tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. C_cg_g_extra_ChapmanLab: C content in cg/g of extra leaf tissues analyzed at Jen Funk's lab at Chapman. Allowable values: Non-negative decimal values, NA. N_cg_g_leaves_UCDavis: N content in cg/g of leaf tissues analyzed at SIF at UC Davis. Allowable values: Non-negative decimal values, NA. C_cg_g_leaves_UCDavis: C content in cg/g of leaf tissues analyzed at SIF at UC Davis. Allowable values: Non-negative decimal values, NA. N_cg_g_stem_UCDavis: N content in cg/g of stem tissues analyzed at SIF at UC Davis. Allowable values: Non-negative decimal values, NA. C_cg_g_stem_UCDavis: C content in cg/g of stem tissues analyzed at SIF at UC Davis. Allowable values: Non-negative decimal values, NA. N_cg_g_root_UCDavis: N content in cg/g of root tissues analyzed at SIF at UC Davis. Allowable values: Non-negative decimal values, NA. C_cg_g_root_UCDavis: C content in cg/g of root tissues analyzed at SIF at UC Davis. Allowable values: Non-negative decimal values, NA. N_cg_g_nodule_UCDavis: N content in cg/g of nodule tissues analyzed at SIF at UC Davis. Allowable values: Non-negative decimal values, NA. C_cg_g_nodule_UCDavis: C content in cg/g of nodule tissues analyzed at SIF at UC Davis. Allowable values: Non-negative decimal values, NA. Licor_leaf_mg_forLMA: Mass in mg of Licor leaf tissue used to calculate leaf mass per area (LMA). Allowable values: Non-negative decimal values, NA. Licor_leaf_cm2_forLMA: Area in cm^2 of Licor leaf tissue used to calculate LMA. Allowable values: Non-negative decimal values, NA. Nadded: N added in mg. Allowable values: Non-negative decimal values, NA. seedN: Estimated amount of N in seeds in mg. Allowable values: Non-negative decimal values, NA. Biomass_mg: Total biomass in mg. Calculated from individual biomass components. Allowable values: Non-negative decimal values, NA. AGB_mg: Total aboveground biomass in mg. Calculated from individual biomass components. Allowable values: Non-negative decimal values, NA. BGB_mg: Total belowground biomass in mg. Calculated from individual biomass components. Allowable values: Non-negative decimal values, NA. NtoBiomass: Nodule biomass divided by total biomass. Calculated from individual biomass components. Allowable values: Non-negative decimal values, NA. ThorntoBiomass: Thorn biomass divided by total biomass. Calculated from individual biomass components. Allowable values: Non-negative decimal values, NA. N_mg_leaves: Nitrogen mass in mg in leaves. Allowable values: Non-negative decimal values, NA. N_mg_stem: Nitrogen mass in mg in stems. Allowable values: Non-negative decimal values, NA. N_mg_thorn: Nitrogen mass in mg in thorns. Allowable values: Non-negative decimal values, NA. N_mg_root: Nitrogen mass in mg in roots. Allowable values: Non-negative decimal values, NA. N_mg_nodule: Nitrogen mass in mg in nodules. Allowable values: Non-negative decimal values, NA. N_mg_licor: Nitrogen mass in mg in Licor leaves. Allowable values: Non-negative decimal values, NA. N_mg_extra: Nitrogen mass in mg in extra leaves. Allowable values: Non-negative decimal values, NA. C_mg_leaves: Carbon mass in mg in leaves. Allowable values: Non-negative decimal values, NA. C_mg_stem: Carbon mass in mg in stems. Allowable values: Non-negative decimal values, NA. C_mg_thorn: Carbon mass in mg in thorns. Allowable values: Non-negative decimal values, NA. C_mg_root: Carbon mass in mg in roots. Allowable values: Non-negative decimal values, NA. C_mg_nodule: Carbon mass in mg in nodules. Allowable values: Non-negative decimal values, NA. C_mg_licor: Carbon mass in mg in Licor leaves. Allowable values: Non-negative decimal values, NA. C_mg_extra: Carbon mass in mg in extra leaves. Allowable values: Non-negative decimal values, NA. N_mg_combined: Nitrogen mass in mg in all tissues combined. Allowable values: Non-negative decimal values, NA. C_mg_combined: Carbon mass in mg in all tissues combined. Allowable values: Non-negative decimal values, NA. newNAP15N: Atom % 15N in newly-acquired N, i.e., not seed N. Allowable values: Non-negative decimal values, NA. fseed: Fraction of biomass that was seeds. refAP15N_mean: Arithmetic mean of the atom % 15N values of the reference plants for this individual. Only relevant for inoculated plants. The reference plants are the non-nodulated healthy uninoculated plants of the same species and fertilization treatment. Allowable values: Non-negative decimal values, NA. refAP15N_sd: Standard deviation of the atom % 15N values of the reference plants for this individual. Only relevant for inoculated plants. The reference plants are the non-nodulated healthy uninoculated plants of the same species and fertilization treatment. Allowable values: Non-negative decimal values, NA. Ndfa_mean: Mean estimate of %Ndfa (percent of nitrogen derived from fixation activity as opposed to soil N uptake) for this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. Ndfa_LCI: Lower 95% confidence interval of %Ndfa for this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. Ndfa_UCI: Upper 95% confidence interval of %Ndfa for this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. Ndfa_sd: Standard deviation of %Ndfa for this individual. Only relevant for inoculated plants. Allowable values: non-negative decimal values, NA. SNF_mg_N_mean: Mean estimate of nitrogen fixed (mg N) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_LCI: Lower 95% confidence interval nitrogen fixed (mg N) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_UCI: Upper 95% confidence interval nitrogen fixed (mg N) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_sd: Standard deviation of nitrogen fixed (mg N) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_per_g_C_per_y_mean: Mean estimate of nitrogen fixation rate (mg N per g C per year) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_per_g_C_per_y_LCI: Lower 95% confidence interval of nitrogen fixation rate (mg N per g C per year) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_per_g_C_per_y_UCI: Upper 95% confidence interval of nitrogen fixation rate (mg N per g C per year) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_per_g_C_per_y_sd: Standard deviation of nitrogen fixation rate (mg N per g C per year) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_per_g_nodule_per_hr_mean: Mean estimate of nitrogen fixation rate (mg N per g nodule per hour) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_per_g_nodule_per_hr_LCI: Lower 95% confidence interval of nitrogen fixation rate (mg N per g nodule per hour) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_per_g_nodule_per_hr_UCI: Lower 95% confidence interval of nitrogen fixation rate (mg N per g nodule per hour) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. SNF_mg_N_per_g_nodule_per_hr_sd: Standard deviation of nitrogen fixation rate (mg N per g nodule per hour) by this individual. Only relevant for inoculated plants. Allowable values: decimal values, NA. LicorLeafLMA_g_m2: Leaf mass per area (LMA) in g per m^2. Allowable values: Non-negative decimal values, NA. ``` ## Code/software 2\. The code files are as follows: The code files themselves are well commented, so this README will not go into detail about each one. Rather, it will give an overview of all the files. NSF_GX1_Allocation_PlottingFunctions.R is called from the other two. It provides the code for some of the plotting functions used to make the figures. NSF_GX1_Allocation_Stats_pNdfa.R is the main analysis file. It calculates the needed variables from the data, runs the statistics that are presented in the main paper, and makes the figures that are presented in the main paper. NSF_GX1_Allocation_Stats_tNdfa.R is the analysis file for the alternate analysis that is presented in the supplemental materials. 3\. The data and analysis files match to the display items as shown in the following table. Display Description Analysis code file(s) Main text equations NSF_GX1_Allocation_Stats_pNdfa.R Table 1 Significance table NSF_GX1_Allocation_Stats_pNdfa.R Table 2 Random intercepts NSF_GX1_Allocation_Stats_pNdfa.R Fig. 1 Barnard data NSF_GX1_Allocation_Stats_pNdfa.R Fig. 2 UC Davis data NSF_GX1_Allocation_Stats_pNdfa.R Supplemental text equations NSF_GX1_Allocation_Stats_tNdfa.R Table S1 Species list N/A Table S2 Growing conditions N/A Table S3 Alt Table 1 NSF_GX1_Allocation_Stats_tNdfa.R Table S4 Alt Table 2 NSF_GX1_Allocation_Stats_tNdfa.R