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Data from: More diverse rhizobial communities can lead to higher symbiotic nitrogen fixation rates, even in nitrogen-rich soils

Cite this dataset

Taylor, Benton; Komatsu, Kimberly (2024). Data from: More diverse rhizobial communities can lead to higher symbiotic nitrogen fixation rates, even in nitrogen-rich soils [Dataset]. Dryad. https://doi.org/10.5061/dryad.qrfj6q5qp

Abstract

Symbiotic nitrogen fixation (SNF) by legumes and their rhizobial partners is one of the most important sources of bioavailable nitrogen to terrestrial ecosystems. While most work on the regulation of SNF has focused on abiotic drivers such as light, water, and soil nutrients, the diversity of rhizobia with which an individual legume partners may play an important but under-recognized role in regulating nitrogen inputs from SNF. By experimentally manipulating the diversity of rhizobia available to legumes, we demonstrate that rhizobial diversity can increase average SNF rates by more than 90%, and that high rhizobial diversity can induce increased SNF even under conditions of high soil N fertilization. However, the effects of rhizobial diversity, the conditions under which diversity effects were strongest, and the likely mechanisms driving these diversity effects differed between the two legume species we assessed. These results provide evidence that biodiversity-ecosystem function relationships can occur at scales of an individual plant, and that the effects of rhizobial diversity may be as important as long-established abiotic factors, such as nitrogen availability, in driving terrestrial nitrogen inputs via SNF.

README: More diverse rhizobial communities can lead to higher symbiotic nitrogen fixation rates, even in nitrogen-rich soils

https://doi.org/10.5061/dryad.qrfj6q5qp

Description of the data and file structure

This repository contains three files with data and corresponding code related to a greenhouse experiment where two legume species were exposed to different treatments of nitrogen fertilization and rhizobial diversity. Numerous metrics of plant growth and nitrogen fixation were measured. The "biomass" data file contains biomass data on all ~1,100 plants in the experiment. The "Nfix data" file contains data on the subset of individuals in each treatment that were sent for 15N isotopic analysis to calculate N fixation at the end of the experiment. The R code file requires both data files to run completely. 

Data File 1: Rhizdiv_postprocess_biomass_data_1-2023.csv

This file contains biomass data for all 1100 plants in the experiment. Percent foliar N and atom % 15N data are available for the subset of plants used to estimate nitrogen fixation. Missing data code- NA

Position: Unique position in the greenhouse (1-1100)

Pot: Unique Plant Identifier

Species: Legume species. UE = Ulex europaea, SJ = Spartium junceum

fert: Fertilization treatment in g/m2/yr N delivered as ammonium nitrate

div: Diversity (taxa richness) of rhizobial bacteria used to innoculate the plant (C=no rhizobia Inoculum)

bac: The identities of the rhizobia used to inoculate the plants

harvest.date: Date the plant was harvested at the end of the experiment

stem.biomass: biomass of all aboveground tissue (g)

root.biomass: biomass of all belowground tissue (g)

nodule.number: number of individual nodules found on the entire root system

Rack..: Rack number where the plant's pot was held in the greenhouse. 

Observer: Initials of the researcher harvesting the individual plant

fert.num: Numeric variable for the fertilization treatments

div.num: Numeric variable for the rhizobial diversity treatments

tot.biomass: total biomass of the entire plant (g)

agbg: aboveground to belowground biomass ratio (unitless)

perc.ag: percent of plant's biomass held aboveground (%)

perc.bg: percent of plant's biomass held belowground (%)

XN: Percent nitrogen in leaf material (%)

X15N: Atom percent 15N in leaf nitrogen used to calculate N fixation (atm%)

Data File 2: Rhizdiv_DRYAD_Nfix data_6-2024.csv

Position: Unique position in the greenhouse (1-1100)

Pot: Unique Plant Identifier

Species: Legume species. UE = Ulex europaea, SJ = Spartium junceum

fert: Fertilization treatment in g/m2/yr N delivered as ammonium nitrate

div: Diversity (taxa richness) of rhizobial bacteria used to innoculate the plant (C=no rhizobia Inoculum)

bac: The identities of the rhizobia used to inoculate the plants

harvest.date: Date the plant was harvested at the end of the experiment

stem.biomass: biomass of all aboveground tissue (g)

root.biomass: biomass of all belowground tissue (g)

nodule.number: number of individual nodules found on the entire root system

Rack..: Rack number where the plant's pot was held in the greenhouse. 

Observer: Initials of the researcher harvesting the individual plant

fert.num: Numeric variable for the fertilization treatments

div.num: Numeric variable for the rhizobial diversity treatments

tot.biomass: total biomass of the entire plant (g)

agbg: aboveground to belowground biomass ratio (unitless)

perc.ag: percent of plant's biomass held aboveground (%)

perc.bg: percent of plant's biomass held belowground (%)

XN: Percent nitrogen in leaf material (%)

X15N: Atom percent 15N in leaf nitrogen used to calculate N fixation (atm%)

X15Nsoil.mn: Mean of the distribution calculated for the atm % of soil 15N for the plant. Values estimated independently for each fertilization treatment

X15Nsoil.sd: Standard deviation of the distribution calculated for the atm % of soil 15N for the plant. Values estimated independently for each fertilization treatment

Ndfa: Mean of the calculated value for the percent of the plant's nitrogen derived from fixation activity (%Ndfa). This is the primary estimate of N fixation.

Ndfa_sd: Standard Deviation of the distribution for the calculated value for the percent of the plant's nitrogen derived from fixation activity (%Ndfa).

Ndfa_LCI: Lower 95% Confidence Interval of the distribution for the calculated value for the percent of the plant's nitrogen derived from fixation activity (%Ndfa).

Ndfa_UCI: Upper 95% Confidence Interval of the distribution for the calculated value for the percent of the plant's nitrogen derived from fixation activity (%Ndfa).

File #3 - Analytical R Code. Rhizobial_Diversity_Stats_and_Figures_For_Submission.R:

This file has all statistical and figure creation code presented in the approximate order that is appears in the accompanying manuscript. The code only requires the above-described data files to run (as well as packages loaded internally).

Sharing/Access information

Please contact Dr. Benton Taylor (bentontaylor@fas.harvard.edu) to discuss future publication with these data

Code/Software

One R script file is included that requires both data files to run. Code is annotated and ordered to mirror how the analyses are presented in the corresponding manuscript. 

Methods

Data were collected from a greenhouse experiment conducted at the Smithsonian Environmental Research Center in 2019. Two legume species (Spartium junceum and Ulex europaeus) were exposed to different levels of rhizobial diversity (0 to 5 rhizobial taxa) and different levels of nitrogen fertilization (0 to 20 g/m2/yr). Data represent biomass, biomass allocation, and nitrogen fixation metrics measured on 1100 plants following a five-month growth period.

Funding

Smithsonian Institution