Data from: The evolutionary genomics of adaptation to stress in wild rhizobium bacteria
Data files
Feb 28, 2024 version files 2.74 MB
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20_Ni_island_regions_growth_data_KJ2.csv
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C089B_wt_del_tradeoffs_data_KJ2.csv
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Delgado_Meso_Mastersheet_by_Replicate_2023-11-14_1.csv
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Delgado_Meso_Mastersheet_by_Strain_2023-11-14_1.csv
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GWAS_results.csv
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nreAXY_allele_tolerance_growth_assay_KJ_10.25.2023.2.csv
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README.md
Abstract
Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.
README: Data from: The evolutionary genomics of adaptation to stress in wild rhizobium bacteria
Brief summary of dataset contents: rhizobia phenotypes by strain and replicate within strain as well as soil chemical and ecological characteristics for the soils rhizobia were collected from
Description of the data and file structure
This data supports the manuscript Kehlet-Delgado et al (in prep) The evolutionary genomics of adaptation to stress in wild rhizobium bacteria
Abstract: Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. We demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles associate with distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.
Delgado_Meso_Mastersheet_by_Replicate_2023-11-14.csv
Here are metadata that describe each column in the datasets:
Note: column names with the suffix "_mean" are Mesorhizobium strain mean values for that phenotype, averaged across all Replicates. NA means no data.
Column Description
Unique.ID unique identifier for Mesorhizobium strain
Reserve natural reserve where the strain was collected
Site site within reserve where the strain was collected
Subsite.Strain subsite within site where the strain was collected; typically A, B, or C, but X = no subsite at this site
Subsite.Soil subsite within site where soil was collected and used to match soil data to this strain; typically the same as Strain.Site but may differ
PlantSpecies.Strain plant species from which the strain was isolated; b = Acmispon brachycarpus; w = A. wrangelianus; p = A. parviflorus
PlantSpecies.Soil plant species associated with the site/subsite where soil was collected and used to match soil data to this strain
CollectionDate date when strain's plant host was collected from the field
Waypoint GPS waypoint corresponding to plant sampling location for this strain
Lat latitude where strain was collected
Lon longitude where strain was collected
Elev elevation (in feet) where strain was collected
GenoData indicates if strain has nre genotype data
PhenoData indicates if strain has any phenotypic data
Sequenced indicates if strain was sequenced
Clade clade to which this strain belongs
nreA whether or not nreA was detected in this strain's genome
nreX whether or not nreX was detected in this strain's genome
nreY whether or not nreY was detected in this strain's genome
nreA_alleles identity of detected nreA alleles in strain's genome; different alleles are separated by commas
nreX_alleles identity of detected nreX alleles in strain's genome; different alleles are separated by commas
nreY_alleles identity of detected nreY alleles in strain's genome; different alleles are separated by commas
Replicate replicate for phenotypic measurements; typically ranges 1-3 but some strains have more or fewer replicates
UV.MITassay identifier for individual UV minimum inhibitory time (MIT) assay
UV.MITwell identifier for individual UV minimum inhibitory time (MIT) plate well within an assay
UV.MIT UV minimum inhibitory time in seconds; column names ending in _mean show means for strain across Replicates
Ni.MICassay identifier for individual nickel minimum inhibitory concentration (MIC) assay
Ni.MICwell identifier for individual nickel minimum inhibitory concentration (MIC) plate well within an assay
Ni.MIC Nickel minimum inhibitory concentration in mM; column names ending in _mean show means for strain across Replicates
Co.MICassay identifier for individual cobalt minimum inhibitory concentration (MIC) assay
Co.MICwell identifier for individual cobalt minimum inhibitory concentration (MIC) plate well within an assay
Co.MIC Cobalt minimum inhibitory concentration in mM; column names ending in _mean show means for strain across Replicates
Cr.MICassay identifier for individual chromium minimum inhibitory concentration (MIC) assay
Cr.MICwell identifier for individual chromium minimum inhibitory concentration (MIC) plate well within an assay
Cr.MIC Chromium minimum inhibitory concentration in mM; column names ending in _mean show means for strain across Replicates
GrowthAssayPlate identifier for individual growth assay plate where strain growth in nickel was tested
y0.no initial optical density of strain in the absence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
y0_lm.no initial optical density of the linear model used to predict the strain's growth rate in the absence of nickel (no); output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
mumax.no maximum growth rate for strain in absence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
lag.no lag time of strain in absence of nickel; defined as x-axis corodinate of intersection between maxium slope regression line from fit_alleasylinear() and initial optical density, output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
r2.no coefficient of determination for linear model used to estimate strains's max growth rate in absence of nickel, output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
AUC.no area under the growth curve in absence of nickel, calculated with trapezoid rule; column names ending in _mean show means for strain across Replicates
ODf.no final optical density in absence of nickel; column names ending in _mean show means for strain across Replicates
ODmax.no maximum OD in absence of nickel; column names ending in _mean show means for strain across Replicates
OD72hr.no optical density of strain in absence of nickel, 72 hours post-inoculation; column names ending in _mean show means for strain across Replicates
y0.ni initial optical density of strain in the presence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
y0_lm.ni initial optical density of the linear model used to predict the strain's growth rate in the presence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
mumax.ni maximum growth rate for strain in presence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
lag.ni lag time of strain in presence of nickel; defined as x-axis corodinate of intersection between maxium slope regression line from fit_alleasylinear() and initial optical density, output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
r2.ni coefficient of determination for linear model used to estimate strains's max growth rate in presence of nickel, output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
AUC.ni area under the growth curve in presence of nickel, calculated with trapezoid rule; column names ending in _mean show means for strain across Replicates
ODf.ni final optical density in presence of nickel; column names ending in _mean show means for strain across Replicates
ODmax.ni maximum OD in presence of nickel; column names ending in _mean show means for strain across Replicates
OD72hr.ni optical density of strain in presence of nickel, 72 hours post-inoculation; column names ending in _mean show means for strain across Replicates
OD72hrRatio (OD72hr.ni - OD72hr.no)/OD72hr.no; column names ending in _mean show means for strain across Replicates
Ni.ppm soil nickel (ppm) matched to this strain; see Merge.Notes for details
CA.MG.RATIO soil calcium:magnesium ratio matched to this strain; see Merge.Notes for details
SerpentineType soil type matched to this strain; serpentine if CA.MG.RATIO is less than 1; nonserpentine if CA.MG.RATIO is greater than 1
Ni.ppm.A/C/X soil nickel from the A, C, or X subsites associated with this strain's Site
CA.MG.RATIO.A/C/X soil Ca:Mg ratio from the A, C, or X subsites associated with this strain's Site
Ni.CV coefficient of variation for the soil nickel at this strain's site; calculated for strains with multiple soil measures per site
CaMg.CV coefficient of variation for the soil Ca:Mg ratio at this strain's site; calculated for strains with multiple soil measures per site
SAMPLEID soil sample ID submitted to A&L Western for chemical analysis
OM organic matter of soil matched to strain
ENR estimated nitrogen release of soil matched to strain, from A&L Western soil analysis
CEC cation exchange capacity of soil matched to strain, measured in milliequivalents per 100g soil, from A&L Western soil analysis
NO3_N nitrate nitrogen (ppm) of soil matched to strain, from A&L Western soil analysis
P1 Weak Bray phosphorus (ppm) of soil matched to strain, from A&L Western soil analysis
HCO3_P Olsen (sodium bicarbonate) phosphorus (ppm) of soil matched to strain, from A&L Western soil analysis
PH soil pH measured off a saturated paste using deionized water, from A&L Western soil analysis
BUFFER_PH measure of both active and reserve acidity in soil, measured off a Sikora buffer solution that mimics that of Shoemaker-McLean-Pratt, from A&L Western soil analysis
S sulfate sulfur (ppm), from A&L Western soil analysis
H soil hydrogen, from A&L Western soil analysis
H_PCT percent cation saturation for H, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
K soil potassium (ppm), from A&L Western soil analysis
K_PCT percent cation saturation for K, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
MG soil magnesium (ppm), from A&L Western soil analysis
MG_PCT percent cation saturation for Mg, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
CA soil calcium (ppm), from A&L Western soil analysis
CA_PCT percent cation saturation for Ca, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
NA. soil sodium (ppm), from A&L Western soil analysis
NA_PCT percent cation saturation for Na, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
AreaCounted area in m2 surveyed for plant host density where strain was sampled in the field
TotalPlantCount total number of the strain's host plant counted in AreaCounted
Notes.Strain notes about strain isolation
Notes.Soil notes about soil sampling
Merge.Notes notes about matching soil data to strain
Storage.note indicates any problems with strain cryopreservation
Strain.issues indicates other issues with strain
Delgado_Meso_Mastersheet_by_Strain_2023-11-14.csv
Brief summary of dataset contents: Genome and isolation data for strains used in this study. (Dataset S1)
Here are metadata that describe each column in the datasets:
Unique.ID unique identifier for Mesorhizobium strain
Reserve natural reserve where the strain was collected
Site site within reserve where the strain was collected
Subsite.Strain subsite within site where the strain was collected; typically A, B, or C, but X = no subsite at this site
Subsite.Soil subsite within site where soil was collected and used to match soil data to this strain; typically the same as Strain.Site but may differ
PlantSpecies.Strain plant species from which the strain was isolated; b = Acmispon brachycarpus; w = A. wrangelianus; p = A. parviflorus
PlantSpecies.Soil plant species associated with the site/subsite where soil was collected and used to match soil data to this strain
CollectionDate date when strain's plant host was collected from the field
Waypoint GPS waypoint corresponding to plant sampling location for this strain
Lat latitude where strain was collected
Lon longitude where strain was collected
Elev elevation (in feet) where strain was collected
GenoData indicates if strain has nre genotype data
PhenoData indicates if strain has any phenotypic data
Sequenced indicates if strain was sequenced
Clade clade to which this strain belongs
nreA whether or not nreA was detected in this strain's genome
nreX whether or not nreX was detected in this strain's genome
nreY whether or not nreY was detected in this strain's genome
nreA_alleles identity of detected nreA alleles in strain's genome; different alleles are separated by commas
nreX_alleles identity of detected nreX alleles in strain's genome; different alleles are separated by commas
nreY_alleles identity of detected nreY alleles in strain's genome; different alleles are separated by commas
Replicate replicate for phenotypic measurements; typically ranges 1-3 but some strains have more or fewer replicates
UV.MITassay identifier for individual UV minimum inhibitory time (MIT) assay
UV.MITwell identifier for individual UV minimum inhibitory time (MIT) plate well within an assay
UV.MIT UV minimum inhibitory time in seconds; column names ending in _mean show means for strain across Replicates
Ni.MICassay identifier for individual nickel minimum inhibitory concentration (MIC) assay
Ni.MICwell identifier for individual nickel minimum inhibitory concentration (MIC) plate well within an assay
Ni.MIC Nickel minimum inhibitory concentration in mM; column names ending in _mean show means for strain across Replicates
Co.MICassay identifier for individual cobalt minimum inhibitory concentration (MIC) assay
Co.MICwell identifier for individual cobalt minimum inhibitory concentration (MIC) plate well within an assay
Co.MIC Cobalt minimum inhibitory concentration in mM; column names ending in _mean show means for strain across Replicates
Cr.MICassay identifier for individual chromium minimum inhibitory concentration (MIC) assay
Cr.MICwell identifier for individual chromium minimum inhibitory concentration (MIC) plate well within an assay
Cr.MIC Chromium minimum inhibitory concentration in mM; column names ending in _mean show means for strain across Replicates
GrowthAssayPlate identifier for individual growth assay plate where strain growth in nickel was tested
y0.no initial optical density of strain in the absence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
y0_lm.no initial optical density of the linear model used to predict the strain's growth rate in the absence of nickel (no); output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
mumax.no maximum growth rate for strain in absence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
lag.no lag time of strain in absence of nickel; defined as x-axis corodinate of intersection between maxium slope regression line from fit_alleasylinear() and initial optical density, output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
r2.no coefficient of determination for linear model used to estimate strains's max growth rate in absence of nickel, output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
AUC.no area under the growth curve in absence of nickel, calculated with trapezoid rule; column names ending in _mean show means for strain across Replicates
ODf.no final optical density in absence of nickel; column names ending in _mean show means for strain across Replicates
ODmax.no maximum OD in absence of nickel; column names ending in _mean show means for strain across Replicates
OD72hr.no optical density of strain in absence of nickel, 72 hours post-inoculation; column names ending in _mean show means for strain across Replicates
y0.ni initial optical density of strain in the presence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
y0_lm.ni initial optical density of the linear model used to predict the strain's growth rate in the presence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
mumax.ni maximum growth rate for strain in presence of nickel; output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
lag.ni lag time of strain in presence of nickel; defined as x-axis corodinate of intersection between maxium slope regression line from fit_alleasylinear() and initial optical density, output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
r2.ni coefficient of determination for linear model used to estimate strains's max growth rate in presence of nickel, output from growthrates package fit_alleasylinear(); column names ending in _mean show means for strain across Replicates
AUC.ni area under the growth curve in presence of nickel, calculated with trapezoid rule; column names ending in _mean show means for strain across Replicates
ODf.ni final optical density in presence of nickel; column names ending in _mean show means for strain across Replicates
ODmax.ni maximum OD in presence of nickel; column names ending in _mean show means for strain across Replicates
OD72hr.ni optical density of strain in presence of nickel, 72 hours post-inoculation; column names ending in _mean show means for strain across Replicates
OD72hrRatio (OD72hr.ni - OD72hr.no)/OD72hr.no; column names ending in _mean show means for strain across Replicates
Ni.ppm soil nickel (ppm) matched to this strain; see Merge.Notes for details
CA.MG.RATIO soil calcium:magnesium ratio matched to this strain; see Merge.Notes for details
SerpentineType soil type matched to this strain; serpentine if CA.MG.RATIO is less than 1; nonserpentine if CA.MG.RATIO is greater than 1
Ni.ppm.A/C/X soil nickel from the A, C, or X subsites associated with this strain's Site
CA.MG.RATIO.A/C/X soil Ca:Mg ratio from the A, C, or X subsites associated with this strain's Site
Ni.CV coefficient of variation for the soil nickel at this strain's site; calculated for strains with multiple soil measures per site
CaMg.CV coefficient of variation for the soil Ca:Mg ratio at this strain's site; calculated for strains with multiple soil measures per site
SAMPLEID soil sample ID submitted to A&L Western for chemical analysis
OM organic matter of soil matched to strain
ENR estimated nitrogen release of soil matched to strain, from A&L Western soil analysis
CEC cation exchange capacity of soil matched to strain, measured in milliequivalents per 100g soil, from A&L Western soil analysis
NO3_N nitrate nitrogen (ppm) of soil matched to strain, from A&L Western soil analysis
P1 Weak Bray phosphorus (ppm) of soil matched to strain, from A&L Western soil analysis
HCO3_P Olsen (sodium bicarbonate) phosphorus (ppm) of soil matched to strain, from A&L Western soil analysis
PH soil pH measured off a saturated paste using deionized water, from A&L Western soil analysis
BUFFER_PH measure of both active and reserve acidity in soil, measured off a Sikora buffer solution that mimics that of Shoemaker-McLean-Pratt, from A&L Western soil analysis
S sulfate sulfur (ppm), from A&L Western soil analysis
H soil hydrogen, from A&L Western soil analysis
H_PCT percent cation saturation for H, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
K soil potassium (ppm), from A&L Western soil analysis
K_PCT percent cation saturation for K, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
MG soil magnesium (ppm), from A&L Western soil analysis
MG_PCT percent cation saturation for Mg, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
CA soil calcium (ppm), from A&L Western soil analysis
CA_PCT percent cation saturation for Ca, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
NA. soil sodium (ppm), from A&L Western soil analysis
NA_PCT percent cation saturation for Na, computed after converting exchangeable cations in ppm to meq per 100g soil, from A&L Western soil analysis
AreaCounted area in m2 surveyed for plant host density where strain was sampled in the field
TotalPlantCount total number of the strain's host plant counted in AreaCounted
Notes.Strain notes about strain isolation
Notes.Soil notes about soil sampling
Merge.Notes notes about matching soil data to strain
Storage.note indicates any problems with strain cryopreservation
Strain.issues indicates other issues with strain
GWAS_results.csv
Brief summary of dataset contents: Pyseer FAST-lmm GWAS results for presence/absence of genes.
Here are metadata that describe each column in the datasets:
Columnn Description
variant_gene_cluster gene cluster id (ortholog)
gene annotation function predicted through prokka or ncbi CDD search
af_cl1 proportion of clade 1 isolates the variant is present in
af_cl2 proportion of clade 2 isolates the variant is present in
filter-pvalue.mic_cl1_genes association of the variant with the phenotype, unadjusted for population structure. (for clade 1 MIC Ni)
lrt-pvalue.mic_cl1_genes the p-value from the mixed model association, as given by FaST-LMM. (for clade 1 MIC Ni)
beta.mic_cl1_genes the effect size/slope of the variant. For a binary phenotype, exponentiate to obtain the odds-ratio. (for clade 1 MIC Ni)
beta-std-err.mic_cl1_genes the standard error of the fit on beta. (for clade 1 MIC Ni)
variant_h2.mic_cl1_genes the variance in phenotype explained by the variant. The ℎ2 for this variant alone. (for clade 1 MIC Ni)
fdr-adj lrt-pvalue.mic_cl1_genes lrt-pvalue adjusted with p.adj "fdr" function in R (for clade 1 MIC Ni)
filter-pvalue.od_cl1_genes association of the variant with the phenotype, unadjusted for population structure. (for clade 1 growth in Ni)
lrt-pvalue.od_cl1_genes the p-value from the mixed model association, as given by FaST-LMM. (for clade 1 growth in Ni)
beta.od_cl1_genes the effect size/slope of the variant. For a binary phenotype, exponentiate to obtain the odds-ratio. (for clade 1 growth in Ni)
beta-std-err.od_cl1_genes the standard error of the fit on beta. (for clade 1 growth in Ni)
variant_h2.od_cl1_genes the variance in phenotype explained by the variant. The ℎ2 for this variant alone. (for clade 1 growth in Ni)
fdr-adj lrt-pvalue.od_cl1_genes lrt-pvalue adjusted with p.adj "fdr" function in R (for clade 1 growth in Ni)
filter-pvalue.mic_cl2_genes association of the variant with the phenotype, unadjusted for population structure. (for clade 2 MIC Ni)
lrt-pvalue.mic_cl2_genes the p-value from the mixed model association, as given by FaST-LMM. (for clade 2 MIC Ni)
beta.mic_cl2_genes the effect size/slope of the variant. For a binary phenotype, exponentiate to obtain the odds-ratio. (for clade 2 MIC Ni)
beta-std-err.mic_cl2_genes the standard error of the fit on beta. (for clade 2 MIC Ni)
variant_h2.mic_cl2_genes the variance in phenotype explained by the variant. The ℎ2 for this variant alone. (for clade 2 MIC Ni)
fdr-adj lrt-pvalue.mic_cl2_genes lrt-pvalue adjusted with p.adj "fdr" function in R (for clade 2 MIC Ni)
filter-pvalue.od_cl2_genes association of the variant with the phenotype, unadjusted for population structure. (for clade 2 growth in Ni)
lrt-pvalue.od_cl2_genes the p-value from the mixed model association, as given by FaST-LMM. (for clade 2 growth in Ni)
beta.od_cl2_genes the effect size/slope of the variant. For a binary phenotype, exponentiate to obtain the odds-ratio. (for clade 2 growth in Ni)
beta-std-err.od_cl2_genes the standard error of the fit on beta. (for clade 2 growth in Ni)
variant_h2.od_cl2_genes the variance in phenotype explained by the variant. The ℎ2 for this variant alone. (for clade 2 growth in Ni)
fdr-adj lrt-pvalue.od_cl2_genes lrt-pvalue adjusted with p.adj "fdr" function in R (for clade 2 growth in Ni)
C089B_wt_del_tradeoffs_data_KJ2.csv
Brief summary of dataset contents: Optical density readings for testing nreXY deletion mutant
Here are metadata that describe each column in the datasets:
Columnn Description
Strain strain shortname, WT (KJ094) is wild-type C089B and Del (KJ156) is C089B with nreXY deleted
Ni.mM amount of NiCl2 (mM)
OD optical density (600nm)
Rep replicate number
Plate plate assayed, A or B
Time.hr time of OD reading in hours
Strain.ID strain shortname_Ni.mM
nreXY present or absent for nreXY
20_Ni_island_regions_growth_data_KJ2.csv
Brief summary of dataset contents: Growth data for Ni island regions cloned into A. fabrum
Here are metadata that describe each column in the datasets:
Columnn Description
Unique.ID Unique ID of the strains used in the growth assay (see supplemental table S13)
Growth Growth measured as the optical density at 600 nm after 24 hours.
Rep technical replicate of each strain in the growth assay
Ni.mm level of nickel used in the growth assay media
Ni.region region of the Mesorhizobium nickel island (shown in figure 2A) cloned into A. fabrum
nreAXY_allele_tolerance_growth_assay_KJ_10.25.2023.2.csv
Brief summary of dataset contents: Growth data in Ni for cloned strains containing different nreAXY alleles
Here are metadata that describe each column in the datasets:
Columnn Description
Strain strains used in the growth assay (see supplemental table S13)
Strain.desc strain name the nreAXY allele types, in parentheses is the high tolerance (HT) or low tolerance (LT) with the clade of the strain listed after a dash.
Ni.mm level of nickel used in the growth assay media
Rep technical replicate of each strain in the growth assay
Growth Growth measured as the optical density at 600 nm after 24 hours
Methods
Strain isolation and soil analysis. Acmispon wrangelianus and A. brachycarpus were gathered during March 2019 from natural reserves in California and in May 2019 from areas in Oregon. Within reserves, both serpentine and non-serpentine sites were sampled for: 1) plant root nodules, and 2) the soil directly below the plant, if available. Details on strain isolation and soil analysis procedures are in SI Appendix.
Phenotyping Ni tolerance. The minimum inhibitory concentration (MIC) of Ni was determined for 681 field-collected strains of Mesorhizobium by growing the strains on NiCl2 enriched media plates that ranged from 0 mM to 5 mM increasing by 1 mM for each treatment with three replicates. Ni tolerance was also determined by the growth in liquid media containing 0 or 1 mM NiCl2 (OD600). Details of these procedures are in SI Appendix.