Isolation of Streptomycetes

The panel of 18 strains (Supplementary Table 1) used in this study included 13 Streptomyces isolates originating from the same soil sample. This sample was collected from the University of Wisconsin-West Madison Agricultural Research Station on 10 June 2014. The soil in the collection area was composed of Troxel silt loam at 1–3% slopes. A soil core was collected using a sterile 50 ml conical tube (VWR). A 0.25-g piece of soil was extracted from a depth of 4 cm below the surface. This soil was separated into individual grains (∼1 mg), each of which was used to inoculate a Petri dish containing Actinomycete Isolation Agar (4 g l⁻¹ sodium propionate, 10 g l⁻¹ soluble starch, 0.4 g l⁻¹ sodium caseinate, 2 g l⁻¹ KNO₃, 2 g l⁻¹ NaCl, 2 g l⁻¹ K₂HPO₄, 0.05 g l⁻¹ MgSO₄, 0.02 g l⁻¹ CaCO₃, 0.01 g l⁻¹ FeSO₄, 18 g l⁻¹ Agar; pH adjusted to 7.5; to prevent fungal growth, cyclohexamide added after autoclaving to reach 50 mg l⁻¹).

Separated isolates on each Petri dish were automatically detected and pinned into individual wells of a 96-well plate containing Actinomycete Isolation Agar medium using an automatic colony picker (Hudson). To distinguish isolates, we sequenced a 935–base-pair region of their DNA-directed RNA polymerase subunit β (rpoB) gene, which is commonly used as a species-level phylogenetic marker for Streptomyces³³. We identified 28 distinct Streptomyces isolates, and selected 13 for invasion experiments based on having sufficient growth for sustained propagation on the defined medium used in the invasion experiment. These 13 isolates were named by their soil grain and microplate well. For example, sp. S25E2 and sp. S25H8 were both isolated from the same soil grain (S25). The remaining five strains used in this study were collected from various sources (Supplementary Table 1). Using the R³⁴ package DECIPHER³⁵, these 18 strains' rpoB sequences were aligned to those from related species in order to create the phylogenetic tree shown in Supplementary Fig. 1.