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README

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Data from: Heterosis of leaf and rhizosphere microbiomes in field-grown maize

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Please cite this data package (doi: 10.5281/zenodo.3785569) and the corresponding article (dot: 10.1073/pnas.2021965118) if you use the contents for your own work.

DATASET CITATION:
Wagner, Maggie R.; Tang, Clara; Salvato, Fernanda; Clouse, Kayla M.; Bartlett, Alexandria; Vintila, Simina; Phillips, Laura; Sermons, Shannon; Hoffmann, Mark; Balint-Kurti, Peter J.; Kleiner, Manuel (2020). Data from: Microbe-dependent heterosis in maize [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3785569

ARTICLE CITATION: 
Wagner, Maggie R.; Tang, Clara; Salvato, Fernanda; Clouse, Kayla M.; Bartlett, Alexandria; Vintila, Simina; Phillips, Laura; Sermons, Shannon; Hoffmann, Mark; Balint-Kurti, Peter J.; Kleiner, Manuel (2021). Microbe-dependent heterosis in maize. PNAS July 27, 2021 118 (30) e2021965118; https://doi.org/10.1073/pnas.2021965118

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DIRECTORY STRUCTURE

1. README.rtf (this file)
2. Expt1_data.txt (tab-delimited text file)
3. SynCom_germination_data.txt (tab-delimited text file)
4. Expt2_data.txt (tab-delimited text file)
5. Expt2_seedWeights_sorted.txt (tab-delimited text file)
6. Expt2_soil_data_TAMU.txt  (tab-delimited text file)
7. Expt3_biomass.txt (tab-delimited text file)
8. Expt3_germ_growth.txt (tab-delimited text file)
9. Pythium_data.xlsx (Excel spreadsheet)
10. mdh_analysis.R (R script)
11. Expt3_viability.txt (tab-delimited text file)
12. fum_16S_ITS.zip (archive)
13. Expt4_data.xlsx (Excel spreadsheet)
14. SynCom_colonization_data.xlsx (Excel spreadsheet)

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####### 2. Expt1_data.txt (tab-delimited text file)
Data from Experiment #1 (growth chamber; synthetic community vs. sterile buffer)

PlantID = unique identifier for one plant
Treatment = "syncom" for plants inoculated with the synthetic bacterial community. “Sterile” for plants that received sterile phosphate-buffered saline (PBS)
Category = hybrid or inbred
Genotype = B73, Mo17, or B73xMo17
Leaf_Number = number of leaves at time of sampling
WholePlant_g = fresh weight (in grams) of entire plant
Shoot_g = fresh weight (in grams) of plant after root was removed
Germ = 1 for seeds that germinated; 0 for seeds that did not germinate

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####### 3. SynCom_germination_data.txt (tab-delimited text file)
Data from a separate follow-up experiment to assess the effect of the synthetic bacterial community on germination.

ID = unique identifier for each experimental replicate (i.e. Petri dish with 5 seeds)
Genotype = B73, Mo17, or B73xMo17
Nutrient = nutrient solution used to hydrate seeds: Water, MS, or Hoagland
Community = “Syncom" for plants inoculated with the synthetic bacterial community. “Control” for plants that received sterile phosphate-buffered saline (PBS)
Rate = percent germination after 4 days
Rate_11 = percent germination after 11 days

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####### 4. Expt2_data.txt (tab-delimited text file)
Data from Experiment #2 (growth chamber; live soil slurry, autoclaved soil slurry, or sterile PBS)

PlantID = unique identifier for one plant
Genotype = B73, Mo17, or B73xMo17
Treatment = “live” for live soil slurry, “killed” for autoclaved soil slurry, “control” for sterile PBS
Treatment2 = more descriptive version of Treatment
Germ = Y for seeds that germinated; N for seeds that did not germinate
Total_mass_g = fresh weight (in grams) of entire plant
Shoot_mass_g = fresh weight (in grams) of plant after root was removed

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####### 5. Expt2_seedWeights_sorted.txt (tab-delimited text file)
Weights of kernels used for Experiment #2, and their even assortment into 3 treatments.

Row, Col = location of kernel in plate
Genotype = B73, Mo17, or B73xMo17
mass_g = weight of the kernel in grams
Treatment = the microbial treatment group to which each kernel was assigned: “Control” for sterile PBS; “Killed_Soil” for autoclaved soil slurry; “Live_Soil” for live soil slurry

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####### 6. Expt2_soil_data_TAMU.txt  (tab-delimited text file)
Data on abiotic properties of the calcined-clay growth medium in Experiment #2. Data generated by the Texas A&M AgriLife Extension Service Soil, Water, and Forage Testing Laboratory (soiltesting.tamu.edu)

SampleID = unique identifier for one soil sample, which was a composite of 2-3 gnotobiotic growth bags in which the kernel did not germinate
Treatment = “live” for live soil slurry, “killed” for autoclaved soil slurry, “control” for sterile PBS
Cond_umhos_per_cm = conductivity (measured in micromhos per cm)
*_ppm = concentration in parts per million of macro/micro nutrients

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####### 7. Expt3_biomass.txt (tab-delimited text file)
Root and shoot biomass data from Experiment #3 (field experiment, untreated vs. fumigated soils). Biomass data was collected for 3 of the 5 treatments.

PlantID = unique identifier for one plant; links to Expt3_germ_growth.txt
root_dry_weight_g = weight in grams of oven-dried root system
shoot_dry_weight_g = weight in grams of oven-dried shoots

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####### 8. Expt3_germ_growth.txt (tab-delimited text file)
Plant growth data from Experiment #3 (North Carolina field experiment, untreated vs. fumigated soils). 

PlantID = unique identifier for one plant; links to Expt3_biomass.txt
UNQID = another unique identifier
Idnum = simple unique identifier
Genotype = B73, Mo17, or B73xMo17
Source = which batch of kernels was used
Treatment =  “control” for untreated field soil; “AITC_only” for allyl isothiocyanate fumigation; “steam_only” for steam treatment;  “AITC_steam” for combined AITC fumigation and steam treatment; “chloropicrin” for chloropicrin fumigation
Block, Sub_block, Position, Sub_row = details on physical location of plant in experiment
rand = meaningless random number used to randomize plant locations
Germ_NN_dap = germination status NN days after planting. 1 for plants that emerged; 0 for plants that did not emerge
Leaf_Number_NN_dap = number of leaves NN days after planting
Height_cm_NN_dap = height (in cm) NN days after planting

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####### 9. Pythium_data.xlsx (Excel spreadsheet)
Data on efficacy of fumigation treatments in Experiment #3 (field experiment, untreated vs. fumigated soils). 

WORKSHEET ‘PPG’
Replicate = unique sample ID
Treatment =  “NTC” for untreated field soil; “AITC” for allyl isothiocyanate fumigation; “Steam” for steam treatment;  “Steam & AITC” for combined AITC fumigation and steam treatment; “Pichlor” for chloropicrin fumigation
ppg/g soil = measured propagules of Pythium spp. per gram soil

WORKSHEETS ‘TEMP STEAM’ AND ‘TEMP STEAM + AITC’
# = unique identifier for each observation
Time = real time of observation
Surface = temperature (in degrees C) at soil surface
N inches depth = temperature (in degrees C) N inches below soil surface
 
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####### 10. mdh_analysis.R (R script)
R code used for data analysis and figure generation.

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####### 11. Expt3_viability.txt (tab-delimited text file)
Data from culture-based tests of microbial viability after soil fumigation treatments in Experiment #3.

ID = unique identifier for replicate soil sample
Week = time of sample collection (weeks post soil treatment)
Plate = microbial growth media (Vxyl G or R2A)
Rep = replicate (within treatment)
Depth = S for shallow soil layer; D for deep soil layer
Treat = soil treatment. “UT” for untreated field soil; “AITC” for allyl isothiocyanate fumigation; “STE” for steam treatment;  “AITC_STE” for combined AITC fumigation and steam treatment; “STND” for chloropicrin fumigation
logCFU = log-transformed CFU counts

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####### 12. fum_16S_ITS.zip
Archive containing processed 16S and ITS amplicon data (i.e., ASV tables) from the soil fumigation experiment. In addition, it contains all code and accessory files used to process and analyze the sequence data. The archive contains its own readme.txt with details on the files and their usage.

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####### 13. Expt4_data.xlsx
Plant growth data from Experiment #4 (Kansas field experiment, untreated vs. steamed soil).

ALL WORKSHEETS
ID = unique plant identifier
Genotype = B73, Mo17, or B73xMo17
Treatment = steamed_soil or untreated_soil
Block = physical location of each plant in the experiment

 WORKSHEET ‘dry_weight’
Shoot_weight = dry weight (g) of aboveground plant parts at end of experiment
Root_weight = dry weight (g) of belowground plant parts at end of experiment

WORKSHEET ‘emergence’
emerge_dayXX = 1 if the plant had emerged XX days after planting; 0 if it had not emerged
cause_of_death = if known, the reason that a plant did not survive after emergence
days_to_emergence = the number of days after planting until a plant emerged
ever_emerged = 1 if the plant emerged within 29 days after planting; 0 if it did not

WORKSHEET ‘plant_height’
MM_DD_2020 = height (in cm) on the DD day of MM month, 2020

WORKSHEET ‘developmental_stage’
MM_DD_2020 = developmental stage on the DD day of MM month, 2020. Developmental stages are as defined in https://crops.extension.iastate.edu/encyclopedia/corn-growth-stages

WORKSHEET ‘chlorophyll_content’
MM_DD_2020 (X) = The Xth out of 3 measurements of chlorophyll concentration (in micromol per square meter) on the DD day of MM month, 2020. 
avg_MM_DD_2020 = The average of the three chlorophyll concentration measurements taken on the DD day of MM month, 2020.  

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####### 14. SynCom_colonization_data.xlsx 

WORKSHEET ‘raw_data’ 
# Contains measured colonization rates by each bacterial strain in the SynCom, in the roots of four maize genotypes (“Sugarbun”, “B73”, “Mo17”, and “B73 x Mo17”). Results of 4 independent replicates are presented for each strain in each maize genotype.
# Strains are abbreviated: SMA = Stenotrophomonas maltophilia; OPI = Ochrobactrum pituitosum; CPU = Curtobacterium pusillum; ECL = Enterobacter cloacae; CIN = Chryseobacterium indologenes; HFR = Herbaspirillum frisingense; PPU = Pseudomonas putida.
CFU (10uL) = the number of colony-forming units (CFU) observed after plating 10uL of the diluted suspension
CFU/mL = the observed number of CFU from 10uL, multiplied by 100 to estimate the number of CFU n 1000 uL
Dilution factor = how diluted was the 10uL suspension plated?
Root Fresh Weight (g) = grams of harvested root from which the replicate measurement was made
CFU/ g FW = estimated CFU standardized per g of root fresh weight
“Average” = the average CFU/ g FW of the 4 replicates for each strain in each genotype
“STDAV” = the standard deviation of CFU/ g FW of the 4 replicates for each strain in each genotype
“Total bacterial cells” = the sum of all strains’ CFU/ g FW in a given genotype
“Relative abundance” = the strain’s CFU/ g FW divided by Total bacterial cells for the same genotype

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Additional questions about this data package should be directed to maggie.r.wagner@gmail.com 
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