DOI: 10.5061/dryad.x3ffbg7rm
title: Is there a latitudinal diversity gradient for symbiotic microbes? A case study with sensitive partridge peas

description: Mutualism is thought to be more prevalent in the tropics than temperate
 zones and may therefore play an important role in generating and
 maintaining high species richness found at lower latitudes. However,
 results on the impact of mutualism on latitudinal diversity gradients are
 mixed, and few empirical studies sample both temperate and tropical
 regions. We investigated whether a latitudinal diversity gradient exists
 in the symbiotic microbial community associated with the legume
 Chamaecrista nictitans. We sampled bacteria DNA from nodules and the
 surrounding soil of plant roots across a latitudinal gradient (38.64 °N to
 8.68 °N). Using 16S rRNA sequence data, we identified many non-rhizobial
 species within C. nictitans nodules that cannot form nodules or fix
 nitrogen. Species richness increased towards lower latitudes in the
 non-rhizobial portion of the nodule community but not in the rhizobial
 community. The microbe community in the soil did not effectively predict
 the non-rhizobia community inside nodules, indicating that host selection
 is important for structuring non-rhizobia communities in nodules. We next
 factorially manipulated the presence of three non-rhizobia strains in
 greenhouse experiments and found that co-inoculations of non-rhizobia
 strains with rhizobia had a marginal effect on nodule number and no effect
 on plant growth. Our results suggest that these non-rhizobia bacteria are
 likely commensals – species that benefit from associating with a host but
 are neutral for host fitness. Overall, our study suggests that temperate
 C. nictitans plants are more selective in their associations with the
 non-rhizobia community, potentially due to differences in soil nitrogen
 across latitude.
description: This dataset includes both 16S sequence data and experimental
 data from manipulative greenhouse experiments. The 16S sequence data was
 collected from microbes extracted from plant root nodules and the
 surrounding soil. Sequencing data was assembled and classified into ASVs
 using QIIME2. The feature tables, taxonomy files, and phylogenies were all
 produced using QIIME2 and were used as the starting files for analysis in
 R. Experiment data was collected on plant individuals grown in the
 greenhouse and growth chambers over 3-4 months. 
description: # Is there a latitudinal diversity gradient for symbiotic microbes? A case
 study with sensitive partridge peas
 [https://doi.org/10.5061/dryad.x3ffbg7rm](https://doi.org/10.5061/dryad.x3ffbg7rm) The following files contain the original data and code required for reproducing the results in this publication. This dataset includes both 16S sequence data and experimental data from manipulative greenhouse experiments. Sequencing data collected from microbes extracted from nodules and the surrounding soil of plant roots was assembled and classified into ASVs using QIIME2. The feature tables, taxonomy files, and phylogenies were all produced using QIIME2 and were used as the starting files for analysis in R. The raw sequence data which has been uploaded to SRA (PRJNA1029754). Experiment data was collected on plant individuals grown in the greenhouse and growth chambers over 3-4 months. All files with the .Rmd extension include the detailed analyses performed in R. Other files included are required for running the .Rmd analyses and detailed explanations are available in the .Rmd scripts. ## Description of data files All .Rmd files include the code needed for reproducing the results. There are four main categories of analyses: 1) cleaning the ASV data (ASV\_filtering\_clean.Rmd), 2) diversity analyses on nodule ASVs (Nodule\_diversity.Rmd), 3) diversity analyses on soil ASVs (Soil\_diversity.Rmd), and 4) greenhouse experiment data (Coinoculation\_experiments.Rmd). The ASV\_filtering\_clean.Rmd analysis should be run first to create the the files needed for input in the Nodule\_diversity.Rmd and Soil\_diversity.Rmd analyses. The Bacillus.csv and Pseudomonas.csv files include information on: * the plant individual in the experiment (Plant\_ID) * plant maternal line (Family) * the experimental treatment (Treatment) * the presence or absence of various microbes (Bradyrhizobium, Pseudomonas Variovorax Bacillus, Rhizobia) * the blocked group in the greenhouse/growth chamber (Block) * position of the plant in the rack (Position) * whether or not the plant individual germinated where 1 indicates the plant did germinate (Germination) * mortality data where 1 indicates the plant is alive (Mortality) * leaf counts on different weeks throughout the experiment (Leaf\_no) * nodule number counted on roots (Nodule\_no) * number of pink nodules (Pink\_nodule) * number of yellow nodules (Yellow\_nodule) * number of dark nodules (Dark\_nodules) * number of long nodules (Long\_nodule) * number of round nodules (Round\_nodule) * number of days until first flower (Flower\_date) * number of total flowers (Flower\_count) * aboveground biomass in mg (Aboveground\_mg) * aboveground biomass in grams (Aboveground\_g) * belowground biomass in grams (Belowground\_g) * belowground biomass in mg (Belowground\_mg) * whether the plant is dead at the end of the experiment where a 1 indicates the plant is dead (Dead) * day of death of plant (Death\_day) * weight of a group of nodules in ug (Nodule\_weight\_ug) * number of nodules weighed for the value in Nodule\_weight\_ug (Nodule\_no\_weighed) All files with .txt extensions are phylogeny files for creating the feature table in R All files with .tsv extensions include metadata for the samples with sequence data (nodule and soil) including geographic locations and population information for culture, field, and soil samples of nodule microbial communities from C. nictitans plants The SubSampleScript.R script is used in the Nodule\_Diversity.Rmd analysis for subsampling ASVs across temperate, subtropical, and tropical regions All .biom and .nwk files are output from qiime needed for loading the ASV data into R All .csv files include ASV codes for filtering the full ASV dataset ## Sharing/Access information Raw sequence data for the QIIME2 analyses can be found on SRA under the BioProject PRJNA1029754 Github repository of the code and data for reproducing the results is also available * https://github.com/harri318/symbiotic-latitudinal-gradients.git