DOI: 10.5061/dryad.612jm64bw
title: Plant adaptation to soil nitrogen: The role of microbes vs. the abiotic environment

description: Local adaptation is widely documented, but contributing selective agents
 are rarely identified or disentangled. Here we partition the effects of
 soil nitrogen and microbes on plant local adaptation. We experimentally
 manipulated both nitrogen and soil microbial communities on twelve
 Amphicarpaea bracteata populations from across a naturally occurring soil
 nitrogen gradient to investigate whether nitrogen and/or microbes
 contribute to local adaptation. We found that plants that had evolved in
 high nitrogen environments shifted resource allocation from mutualism
 (nitrogen-fixing rhizobia) to reproduction when grown in high nitrogen,
 while plants from low nitrogen sites did not, suggesting that
 mutualism-related traits have diverged across the nitrogen gradient.
 However, we detected no evidence for plant local adaptation to soil
 nitrogen or sympatric microbes. We also failed to find evidence for
 microbe-mediated adaptive plasticity (the phenomenon in which microbes
 from a particular habitat promote plant fitness in that habitat); even
 though rhizobia from high nitrogen sites produced more nodules than
 rhizobia from low nitrogen sites in high contemporary nitrogen, this did
 not affect plant fitness. This study shows that despite the large
 ecological effects of nitrogen on plants and plant-microbe interactions,
 soil nitrogen and its effects on microbial communities may not always
 contribute to local adaptation.
description: # Plant adaptation to soil nitrogen: The role of microbes vs. the abiotic
 environment
 [https://doi.org/10.5061/dryad.612jm64bw](https://doi.org/10.5061/dryad.612jm64bw) ## Description of the data and file structure We grew twelve *Amphicarpaea bracteata* populations and four soil microbial communities from across a naturally occurring soil N gradient in three levels of contemporary N to investigate whether soil microbes and N availability contribute to plant local adaptation and whether rhizobium populations are adapted to local hosts and/or N availability. We found that plants with a history of elevated soil N shifted resource investment from mutualism to reproduction when grown in high contemporary N, while investment by plants from low-N sites did not change in response to contemporary N fertilization, suggesting that mutualism-related traits have diverged across the N gradient. However, we detected no evidence for plant local adaptation to microbes or to N. In contrast to plants, rhizobia exhibited local adaptation to high-N soils. Specifically, rhizobia from high-N sites formed more nodules than rhizobia from low-N sites under high contemporary N conditions. For both rhizobium and plant partners, we failed to detect strong coevolutionary interactions leading to the highest fitness for sympatric combinations, but did find significant interactions between plant and microbial populations. Date of data collection: 2019 Geographic location of data collection: Bloomington, IN, USA ### Files and variables #### File: data.csv **Description:**  Fitness data collected from greenhouse-grown plants and the treatments applied to each plant. Missing values are indicated by blank cells. ##### Variables * pot: Pot number the plant was grown in. * seed_ID: Seed family the seed originated from. * pop: Site code of the field population the seed originated from. * plant_N: Concentration of total soil N (ug N/g soil) at the field site where the plant population was collected. * cont_N: Contemporary nitrogen level: the amount of N fertilizer applied to the plant in the greenhouse. low = 4 mL distilled water (0 mg N) applied 3 separate days. medium = 4 mL of 200 mg N/L solution (571 mg ammonium nitrate/L) applied 3 separate days. high = 4 mL of 400 mg N/L solution (1143 mg ammonium nitrate/L) applied 3 separate days. * inoc: Site code where the microbial community inoculated onto the plant was collected. Soil slurries were created by combining 10 mL of soil and 40 mL distilled water. 2 mL of slurry was applied to each plant. control = 2 mL sterilized soil slurry applied to plant. * ag_seeds: Total aerial (aboveground) seeds produced by the plant. * bg_seeds: Total subterranean (belowground) seeds produced by the plant. * ag_wt: Aboveground (shoot) biomass in grams, weighed after drying at 60C for &gt; 3 days. * bg_wt: Belowground (root) biomass in grams, weighed after drying at 60C for &gt; 3 days. * nod_ct: Total nodules counted on the plant's roots. * nod_tube_ct: Number of nodules collected and weighed (used to calculate total nodule weight). * tube_wt: Tare weight in grams of epi tube nodules were collected in (used to calculate total nodule weight). * nod_tube_wt: Mass in grams of epi tube and collected fresh nodules (used to calculate total nodule weight). * scar_date: Date the seed was scarified (not analyzed in manuscript). * sprout_date: Date the plant emerged from the soil (not analyzed in manuscript). * leaf_date: First date the plant had an open true leaf (not analyzed in manuscript). * fruit_date: First date the plant formed a fruit (not analyzed in manuscript). * harvest_date: Date the plant was removed from the greenhouse and harvested (not analyzed in manuscript). * fruit_ct: Total number of fruits produced by the plant (not analyzed in manuscript). * bg_seed_wt: Total mass in grams of subterranean (belowground) seeds produced by the plant, weighed fresh (not analyzed in manuscript). * counted_by: Person who counted and collected nodules (not analyzed in manuscript). #### File: site_data.csv **Description:** Site names and codes with environmental data. Missing values are indicated by blank cells. ##### Variables * site_name: Name of the field site. * site_code: Three-letter abbreviation of the field site name used in the main data file. * soil_N: Concentration of total (nitrate and ammonium) soil N in ug N/g soil at the field site. * soil_h2o: Gravimetric water content measured at the field site. * PAR: Photosynthetically active radiation measured at the field site. * lat: Latitude of the field site in decimal degrees. * long: Longitude of the field site in decimal degrees. * seeds: Whether seeds that originated at the field site were used in the experiment. * soil: Whether soil microbial communities collected at the field site were used in the experiment. ## Code/software **Code file:** code_MC1.R **Description:** The R code script used to clean and tidy the data, perform statistical analyses, and create figures. **Software** R version 4.4.1 (2024-06-14) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Ventura 13.6.9 loaded packages: attached base R packages: * grid * stats * graphics * grDevices * utils * datasets * methods * base other attached packages: * car_3.1-2 * carData_3.0-5 * DHARMa_0.4.6 * dplyr_1.1.4 * emmeans_1.10.3 * ggplot2_3.5.1 * ggpubr_0.6.0 * ggrepel_0.9.5 * ggspatial_1.1.9 * glmmTMB_1.1.9 * mapdata_2.3.1 * maps_3.4.2 * osmdata_0.2.5 * tidyr_1.3.1 * tigris_2.1 ## Access information Data was derived from the following sources: * Field site data from: Suwa, T. (2016). The role of resource mutualism in plant response and adaptation to abiotic environments [Dissertation]. Michigan State University.