Fig. 2: Selection of bacterial and fungal taxa for SynComs based on co-occurrence, NetShift, and random-forest analyses.
From: Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease
a, b Bacterial networks. GH (a) and NF (b) networks are shown. The nodes are colored to indicate different bacterial modules. c, d Fungal networks. GH (c) and NF (d) networks are shown. The nodes are colored to indicate different fungal modules. The correlations were inferred from zOTUs abundance profiles using the Spearman method and only the robust and significant (correlation values <−0.7 or >0.7 and P < 0.001) correlations were maintained for the construction of co-occurrence networks. Each node corresponds to the bacterial or fungal zOTUs, and edges between nodes correspond to either positive (red line) or negative (blue line) correlations. The statistical test used was two-sided. e, f Potential NF keystone taxa determined based on bacterial co-occurrence networks in NF and GH plant microbiomes. Data for bacteria (e) and fungi (f) are shown. Bar plots illustrate comparisons of network edges, vertices, degrees, and average path lengths in NF and GH. The big red nodes were calculated based on scaled NESH score and represent particularly important NF driver taxa. The corresponding taxon names are shown in bold. Red lines indicate node (taxa) connections present only in the NF plant microbiome; green lines indicate associations present only in the GH plant microbiome; and blue lines indicate associations present in both the NF and GH plant microbiomes. g Sixteen biomarker bacterial genera identified by employing random-forest classification of the relative abundance in the tomato rhizosphere. h Eighteen biomarker fungal genera identified by employing random-forest classification of the relative abundance in the tomato rhizosphere. Horizontal length indicates the importance to the accuracy of the random-forest mode. The tenfold cross-validation error and the identified numbers of bacterial biomarkers (i), and fungal biomarkers (j), were used to differentiate field tomato groups from greenhouse tomato groups.
