Figure S3.
Phylogenetic Diversity of Fungal and Oomycetal Culture Collections and Fungal Effect on Plant Growth, Related to Figure 3
(A) Maximum likelihood trees of Sanger-sequenced fungal ITS sequences for all isolates that show non identical ITS or that originate from different sites. Fungal isolates (Mor = Mortierella, Elm = Elmerina, Cop = Coprinopsis, Rhi = Rhizoctonia, Den = Dendryphion, Pho = Phoma, Pyr = Pyrenochaeta, Alt = Alternaria, Pha = Phaseolina, Par = Paraphoma, Mac = Macrophomina, Api = Apiosporina, u.L. = unclassified Leotiomycete, Lep = Leptodontidium, Zal = Zalerion, Tru = Truncatella, Mic = Microdochium, Aso = Asordaria, Cha = Chaetomium, Ver = Verticillium, Ple = Plectosphaerella, Cyl = Cylindrocarpon, Sta = Stachybotrys, Fus = Fusarium, Ily = Ilyonectria, Neo = Neonectria). The first outer ring indicates the origin of each isolate, the second ring shows the number of isolates with 100% sequence identity that were isolated from the same site, therefore representing clonal duplicates. Isolates that were used in the reconstitution experiments are highlighted with red squares.
(B) Maximum likelihood trees of Sanger-sequenced oomycetal ITS sequences for all isolates that show non identical ITS or that originate from different sites. Oomycetal isolates (Phy = Phytium). The first outer ring indicates the origin of each isolate, the second ring shows the number of isolates with 100% sequence identity that were isolated from the same site, therefore representing clonal duplicates. Isolates that were used in the reconstitution experiments are highlighted with red squares.
(C) Effect of individual fungal isolates on A. thaliana growth in the FlowPot system. The boxplots depict normalized fresh weight of A. thaliana Col-0 plant shoots after three weeks of incubation with each of the 34 fungal strains used in the multi-kingdom microbiota reconstitution experiment (see Figure 4). For each boxplot, three biological replicates (depicted with different shapes) with at least three technical replicates are presented. Significant differences are indicated with an asterisk (p < 0.01, Kruskal-Wallis with Dunn’s post hoc test). The 11 fungal strains enriched in the absence of bacteria (depicted in Figure S4E) are highlighted in red and a 23-member fungal community lacking these 11 isolates remains deleterious for plant growth (fungal community-enriched). N.A.: data not available