Cooperation among microbes is important for traits as diverse as antibiotic resistance, pathogen virulence, and sporulation. The evolutionary stability of cooperation against “cheater” mutants depends critically on the extent to which microbes interact with genetically similar individuals. The causes of this genetic social structure in natural microbial systems, however, are unknown. Here we show that social structure among cooperative Dictyostelium amoebae is driven by the population ecology of colonization, growth, and dispersal acting at spatial scales as small as fruiting bodies themselves. Despite the fact that amoebae disperse while grazing, all it takes to create substantial genetic clonality within multicellular fruiting bodies is a few millimeters distance between the cells colonizing a feeding site. Even adjacent fruiting bodies can consist of different genotypes. Soil populations of amoebae are sparse and patchily distributed at millimeter scales. The fine-scale spatial structure of cells and genotypes can thus account for the otherwise unexplained high genetic uniformity of spores in fruiting bodies from natural substrates. These results show how a full understanding of microbial cooperation requires understanding ecology and social structure at the small spatial scales microbes themselves experience.
Data: Spatial distribution of D. discoideum in soil
Abundance of Dictyostelium discoideum isolates in small soil samples collected along transects. See Fortunato et al (2003) Mol Ecol 12:1031 and Gilbert et al (2012) Proc Roy Soc Lond B 279:2619.
data-soil-density.txt
Analysis: Spatial distribution of D. discoideum in soil
Analyze and visualize spatial distribution of Dictyostelium discoideum amoebae among soil samples. Script for use with R environment for statistical computing.
analysis-soil-density.R
Data: D. discoideum plaque growth
Growth of Dictyostelium discoideum plaques on bacterial lawns
data-plaque-growth.txt
Analysis: D. discoideum plaque growth
Analyze and visualize growth of Dictysotelium discoideum plaques on Klebsiella lawns. Script for use with R environment for statistical computing.
analysis-plaque-growth.R
Data: Transect of D. discoideum fruiting bodies across two intersecting plaques
Distribution of genotypes along transect of D. discoideum fruiting bodies across two intersecting plaques.
data-plaque-transect.txt
Analysis: Transect of D. discoideum fruiting bodies across two intersecting plaques
Analyze and visualize distribution of genotypes along transect of Dictyostelium discoideum fruiting bodies across two intersecting plaques. Script for use with R environment for statistical computing.
analysis-plaque-transect.R
Analysis: D. discoideum flow cytometry
Parse flow cytometry .fcs files to determine number and proportion of fluorescent/nonfluorescent Dictyostelium discoideum cells. Script for use with R environment for statistical computing.
count_dicty_cells.R
Data: D. discoideum fruiting bodies sampled from petri plate
Genotype composition of individual Dictyostelium discoideum fruiting bodies sampled from across surface of petri plate. Generated by analysis of flow cytometry data.
data-relatedness.txt
Analysis: D. discoideum fruiting bodies sampled from petri plate
Analyze and visualize distribution of Dictyostelium discoideum genotypes in individual fruiting bodies sampled from across surface of petri plates. Script for use with R environment for statistical computing.
analysis-relatedness.R
Data: Germination of D. discoideum spores on bacterial lawns
Number of plaques observed on bacterial lawns inoculated with known number of Dictyostelium discoideum spores.
data-germination.txt
Data: D. discoideum inocula
Genotype composition of Dictyostelium discoideum samples used to inoculate bacterial lawns. Generated by analysis of flow cytometry data.
data-inocula.txt
Data: Flow cytometry of fruiting bodies from transect across plaques
Raw flow cytometry data (FCS format) from Dictyostelium discoideum fruiting bodies sampled along transect crossing two plaques.
fcs-files-transect.zip
Data: Flow cytometry of D. discoideum inocula and all-RFP controls
Raw flow cytometry data (FCS format) of Dictyostelium discoideum spores (1) inoculated onto bacterial lawns and (2) sampled from fruiting bodies on plates only inoculated with RFP-labelled amoebae.
fcs-files-controls.zip
Data: Flow cytometry of D. discoideum fruiting bodies sampled from across plate
Raw flow cytometry data (FCS format) of Dictyostelium discoideum spores sampled from fruiting bodies on plates inoculated with mix of wild type and RFP-labelled amoebae.
fcs-files-relatedness.zip
Data: D. discoideum microscopy
Individual and composited images of Dictyostelium discoideum fruiting bodies.
dicty-images.zip